Integrated system and process for bioproduct production

ABSTRACT

Processes and systems for production of bioproducts such as biofuels are provided. The bioproduct production processes and systems utilize pretreatment of a carbohydrate-containing feedstock to produce soluble sugar molecules and continuous conversion of the pretreated feedstock to a bioproduct by an immobilized fermenting microorganism.

CROSS-REFERENCE

This application is a continuation application of U.S. Ser. No.12/823,092, filed on Jun. 24, 2010, which claims the benefit of U.S.provisional application Nos. 61/278,932, filed Oct. 13, 2009,61/221,474, filed Jun. 29, 2009 and 61/221,007, filed Jun. 26, 2009, allof which are incorporated herein by reference in their entireties.

FIELD OF THE INVENTION

The invention relates to production of a bioproduct, such as biobutanol,in a continuous microbial fermentation process.

BACKGROUND OF THE INVENTION

Butanol is a high quality fuel and fuel additive. Butanol can be mixed,stored and transported together with gasoline. It has more energy pergallon than ethanol, which translates into better fuel economy forconsumers using butanol blends, and has lower vapor pressure thanethanol, which translates into less ground level pollution. Butanol'slow vapor pressure makes it an attractive low volatility, oxygenated,blend component for refiners to use in complying with stringent vaporpressure specifications. Butanol can provide the oxygenate benefits ofethanol but without undue evaporative emissions, which are a significantsource of air pollution, and at a potentially lower cost. Butanol isalso more hydrophobic than ethanol, i.e., it has a higher tendency torepel water, and is more suitable for blending with gasoline. As such,butanol should be a highly desired component of Reformulated GasolineBlendstock for Oxygenate Blending (RBOB) and California (CARBOB) fuelblendstock. Butanol is also expected to have a reduced life cycleemission of CO₂. Butanol blends should have no detrimental effects onmodern fuel system elastomers, and corrosion and electrical conductivityare expected to be similar to gasoline.

Butanol can also be blended in concentrations in excess of 20% withdiesel fuel. The benefits of addition of oxygenates to diesel fuelinclude the reduction in soot formation, CO, and unburned hydrocarbonemissions. Importantly, addition of butanol to diesel fuel inconcentrations sufficient to realize these benefits retains theflammability rating (flash point) of the diesel fuel without oxygenate.This is a significant benefit to deployment and implementation.

Butanol is also widely used as an industrial chemical. It is used in theproduction of paints, plasticizers, and pesticides, as an ingredient incontact lens cleansers, cement, and textiles, and also as a flavoring incandy and ice cream. The global market for n-butanol was approximately 1billion gallons in 2006; the U.S. market was approximately 300 milliongallons, and is expected to grow approximately 2% per year.

Butanol is currently made from petroleum. Production costs are high andmargins are low, and price trends generally track the price of oil andare heavily influenced by global economic growth.

There is a need for improved methods for production of butanol. Inparticular, methods for environmentally compatible, cost efficient, andenergy efficient production of butanol would be desirable.

BRIEF SUMMARY OF THE INVENTION

Processes and systems for bioproduct production are provided.

In one aspect, a process is provided for producing a bioproduct,including continuously fermenting a microorganism in the presence ofhydrolyzed feedstock of a carbohydrate-containing material. Themicroorganism is immobilized on a support in a bioreactor. Hydrolyzedfeedstock is produced by hydrolysis of the feedstock, which producescarbohydrate molecules that serve as a carbon source for the microbialfermentation. The microorganism continuously converts the hydrolyzedfeedstock into a bioproduct. In some embodiments, the feedstock ishydrolyzed continuously upstream from the bioreactor and the resultinghydrolyzed feedstock is fed continuously to the bioreactor for theduration of the fermentation. In one embodiment, the bioproduct is abiofuel (e.g., butanol, acetone, ethanol). In other embodiments, thebioproduct is a biochemical or a biochemical feedstock, i.e., abiochemical that may be derivatized or converted to another product,e.g., via chemical synthesis. In some embodiments, the bioproduct is asolvent, a biomolecule, an organic acid, an alcohol, a vitamin, a fattyacid, an aldehyde, a lipid, a long chain organic molecule, or a sugaralcohol.

In some embodiments, the hydrolyzed feedstock is fed continuously intomultiple bioreactors arranged in parallel and/or in series, thefermentation occurs continuously in the multiple bioreactors, and themultiple bioreactors contain the same or different microorganism(s). Inone embodiment, the hydrolyzed feedstock is fed continuously intomultiple bioreactors arranged in parallel, the fermentation occurscontinuously in the multiple bioreactors, and the multiple bioreactorscontain the same or different microorganism(s). In another embodiment,the fermentation occurs continuously in multiple bioreactors that arearranged in series, the hydrolyzed feedstock is fed continuously intothe first bioreactor in the series, and effluent from each bioreactor isfed to the next bioreactor downstream in the series. In someembodiments, evolved gas may be removed between series nodes duringoperation of the bioreactors.

In one embodiment, bioreactors are arranged in parallel trains in ahybrid series/parallel arrangement. For example, fermentation mayproceed in multiple bioreactors that are arranged in a combination tooptimize productivity, such as a primary reactor arranged in series witha train of parallel reactors, with hydrolyzed feedstock fed continuouslyinto the first bioreactor in the series and effluent from eachbioreactor fed to the next bioreactor downstream in the series.

In one embodiment, the duration of the fermentation is at least about300 hours. In another embodiment, the duration of the fermentation is atleast about 1000 hours.

In some embodiments, the feedstock is a cellulosic material, forexample, a lignocellulosic material. In some embodiments, the feedstockcontains cellulose and hemicellulose, e.g., lignocellulosic material orwood pulp. In some embodiments, the feedstock is wood selected fromsoftwood, hardwood, or a combination thereof. In some embodiments, thefeedstock is a lignocellulosic material in the form of wood chips,sawdust, saw mill residue, or a combination thereof. In someembodiments, the lignocellulosic material (e.g., wood chips sawdust, sawmill residue, or a combination thereof) is from a feedstock source thathas been subjected to some form of disease or infestation in the growthand/or harvest production period. In one embodiment, the feedstocksource is mountain pine beetle infested pine. In another embodiment, thefeedstock source is sudden oak death syndrome infested oak, e.g.,coastal live oak, tanoak, etc. In another embodiment, the feedstocksource is Dutch elm disease infested elm. In other embodiments, thefeedstock source is lignocellulosic material that has been damaged bydrought or fire.

In some embodiments, lignocellulosic feedstock material is deconstructedprior to hydrolysis. Deconstruction may include one or more processselected from presteaming, mechanical grinding, and mechanicalexplosion. In some embodiments, the feedstock material is deconstructedprior to harvest by a natural or non-natural environmental condition,for example, drought, infestation, fire, and/or herbicide exposure. Insome embodiments, the feedstock material may be deconstructed by adisease organism, for example, mountain pine beetle deconstruction ofpine, sudden oak death syndrome deconstruction of oak, or Dutch elmdisease deconstruction of elm. In some embodiments, lignocellulosicfeedstock material is pretreated to remove extractives. The extractiveremoval pretreatment may include compression, water extraction, solventextraction, alkaline extraction, enzymatic treatment, fungal treatment,oxygen treatment, or air drying. In some embodiments, the pretreatmentto remove extractives may occur prior to or in conjunction withdeconstruction.

In some embodiments, hydrolysis of a feedstock, such as alignocellulosic feedstock, is performed by treatment with an acid. Insome embodiments, the acid includes nitric acid, formic acid, aceticacid, phosphoric acid, hydrochloric acid, or sulfuric acid, or acombination thereof. In one embodiment, the hydrolysis is performed withnitric acid. In another embodiment, the hydrolysis is performed with acombination of nitric acid and acetic acid. In some embodiments, thefeedstock contains acetyl groups and releases acetic acid, resulting inautohydrolysis of hemicellulose, which may then release more aceticacid. This autohydrolysis may be supplemented by addition of a mineralacid, or the amount of mineral acid required for hydrolysis of thefeedstock may be reduced by “leveraging” the natural acetyl content inthe feedstock.

In some embodiments, hydrolysis of a lignocellulosic feedstock isperformed with nitric acid in a process including a first stage and asecond stage, with the second stage hydrolysis performed at a highertemperature than the first stage. In some embodiments, performinghydrolysis at a higher temperature in the second stage decreases orprevents degradation of a desired intermediate product (e.g., monomericsugar molecules). In some embodiments, the conditions in the first stageare chosen to achieve hydrolysis of at least about 70% of thehemicellulose in the feedstock, and the conditions in the second stageare chosen to achieve hydrolysis of at least about 40% of the cellulosein the feedstock. In some embodiments, the feedstock is a hardwood, thefirst stage hydrolysate comprises at least about 60% 5-carbon sugar andat least about 25% 6-carbon sugar, and the second stage hydrolysatecomprises at least about 80% 6-carbon sugar. In some embodiments, thefeedstock is a softwood, the first stage hydrolysate comprises at leastabout 20% 5-carbon sugar and at least about 70% 6-carbon sugar, and thesecond stage hydrolysate comprises at least about 90% 6-carbon sugar.

In some embodiments, lignin is recovered in the residue of the terminalstage, e.g., second stage, of hydrolysis of lignocellulosic feedstock.In one embodiment, the lignin-containing residue is dried to a liquidcontent of about 15% or less. In some embodiments, the lignin-containingresidue is dried to a liquid content of about 35% to about 15%, e.g.,any of about 35%, 30%, 25%, 20%, or 15%, or about 35% to about 30%,about 30% to about 25%, about 25% to about 20%, or about 20% to about15%. In one embodiment, the lignin-containing residue is used as anenergy source for said process. In one embodiment, the lignin-containingresidue is used as a fuel source for electricity generation. In someembodiments, the lignin-containing residue is used as a chemicalprecursor for production of useful products, such as phenolic resins. Insome embodiments, the lignin-containing residue is used as a feed to ananaerobic digestor for production of useful gaseous products, such asmethane or syngas (CO+CH₄). In some embodiments, the lignin-containingresidue is used as a soil enhancer.

In some embodiments, hydrolysis of a feedstock, e.g., lignocellulosicfeedstock, is performed with an acid, e.g., nitric acid, in multiplestages including a first and a second stage, and the multiple, e.g.,first and second, stage hydrolysates are combined prior to introductioninto the bioreactor. In other embodiments, multiple, e.g., first andsecond, stage hydrolysates are introduced as separate hydrolyzedfeedstock streams into separate bioreactors. For example, the firststage hydrolysate is introduced into a first bioreactor and the secondstage hydrolysate is introduced into a second bioreactor, where thefirst and second bioreactors contain the same or differentmicroorganism(s). In one embodiment, the first bioreactor comprises afirst microorganism and the second bioreactor comprises a secondmicroorganism, the first and second microorganisms are different, thefirst microorganism is optimized for growth and/or bioproduct productionon the first stage hydrolysate, and the second microorganism isoptimized for growth and/or bioproduct production on the second stagehydrolysate. In some embodiments, the process includes multiple firstbioreactors in series and/or multiple second bioreactors in series.

In some embodiments, hydrolysis of a feedstock, e.g., lignocellulosicfeedstock is performed with an acid, e.g., nitric acid, in multiplestages including a first stage and a second stage, the first stagehydrolysis occurs in a first hydrolysis module and the second stagehydrolysis occurs in a second hydrolysis module, the resulting secondstage hydrolysate is re-introduced into the first hydrolysis module toproduce a third hydrolysate, and the amount of soluble sugar moleculesin the third hydrolysate is greater than the amount of soluble sugarmolecules in the second stage hydrolysate.

In some embodiments, hydrolysis of a feedstock, e.g., lignocellulosicfeedstock, is performed with an acid, e.g., nitric acid, in multiplestages including a first stage and a second stage, flash steam isgenerated in the first stage hydrolysis, and the flash steam is used todeconstruct the feedstock prior to hydrolysis. In some embodiments,flash steam is generated in the second stage hydrolysis, and the flashsteam is used to deconstruct said feedstock prior to hydrolysis and/orto provide energy for the first stage hydrolysis. In some embodiments,flash steam is generated in the second stage hydrolysis, the flash steamis recompressed, and the recompressed steam is used to provide energyfor the first stage hydrolysis and/or other applications such as, forexample, a downstream distillation process for product purification,such as steam stripping distillation. In some embodiments, flash steamis generated in the second stage hydrolysis, the flash steam is used toprovide energy for a third stage hydrolysis, the temperature of thethird stage hydrolysis is lower than the temperature of the second stagehydrolysis, and the lower temperature permits hydrolysis of remainingoligomeric sugar molecules with less degradation than hydrolysisperformed at a higher temperature.

In some embodiments, hydrolyzed feedstock is conditioned to removeinhibitors of microbial growth and/or bioproduct, e.g., biofuel, forexample, butanol, production prior to introduction of the hydrolyzedfeedstock into the bioreactor, with the conditioning process occurringcontinuously for the duration of the fermentation. In some embodiments,removal of inhibitors includes one or more process selected fromoverliming, adsorption, precipitation, and ion exchange. In oneembodiment, removal of inhibitors is performed by contact of hydrolyzedfeedstock with an ion exchange resin under conditions such that theinhibitors are retained on the resin. In one embodiment, the ionexchange resin is an anion exchange resin. In one embodiment, removal ofinhibitors is performed by precipitation with a metal salt, such as analuminum or iron salt, for example, aluminum sulfate or ferric chloride.In some embodiments, the inhibitors include organic acids, furans,phenols, soluble lignocellulosic materials, extractives, and/or ketones.

In some embodiments, fermentation of the immobilized microorganism isconducted under anaerobic conditions. In one embodiment, themicroorganism is a Clostridium strain. In some embodiments, theClostridium strain is derived from a species selected from Clostridiumsaccharobutylicum, Clostridium saccharoperbutylacetonicum, Clostridiumacetobutylicum, and Clostridium beijerinckii. In some embodiments, theClostridium strain is an environmental isolate or is derived from anenvironmental isolate. In some embodiments, the Clostridium strainpossesses one or more phenotypic characteristics selected from butanoltolerance, tolerance to inhibitors of fermentation, low acidaccumulation, stability in continuous fermentation, high butanol titer,production of biofuel with high butanol to acetone ratio, increasedyield of butanol per unit of feedstock, increased yield of butanol perunit of cellular biomass, increased oxygen tolerance, increased abilityto adhere to a solid support, and decreased ability to sporulate,relative to a wild-type or parent strain from which the Clostridiumstrain is derived, or Clostridium saccharobutylicum B643, Clostridiumsaccharobutylicum P262, Clostridium sacchroperbutylacetonicum N1-4,Clostridium acetobutylicum 824, or Clostridium beijerinckii 8524, grownunder identical conditions.

In some embodiments, the support material on which the microorganism isimmobilized is selected from bone char, polypropylene, steel,diatomaceous earth, zeolite, ceramic, engineered thermal plastic, claybrick, concrete, lava rock, wood chips, polyester fiber, glass beads,Teflon, polyetheretherketone, and polyethylene.

In some embodiments, the immobilized microorganism includes a biofilm.

In some embodiments, the bioreactor in which the immobilizedmicroorganism is grown is in the form of a packed bed, an expanded bed,or a fluidized bed.

In some embodiments, the bioproduct produced in the process includes abiofuel, such as butanol, acetone, ethanol, or a combination thereof. Inone embodiment, the biofuel includes butanol. In one embodiment, butanolis produced by a Clostridium strain.

In some embodiments, the process further includes recovery of thebioproduct, e.g., biofuel, from the fermentation medium. In someembodiments, the recovery process operates continuously for the durationof the fermentation. In some embodiments, the recovery process includesconcentration of the bioproduct. In one embodiment, concentration of thebioproduct includes mechanical vapor recompression.

In some embodiments, the process further includes distillation toseparate the bioproduct, e.g., a biofuel, such as butanol, from othercomponents of the fermentation medium. In one embodiment, flash steamgenerated during hydrolysis of the feedstock provides energy for thedistillation. In one embodiment, butyric acid is recovered in thedistillation, the butyric acid is added to the fermentation medium inthe bioreactor, and the microorganisms in the bioreactor convert thebutyric acid to butanol. In one embodiment, the bioproduct is butanol,butyric acid is recovered in the distillation, the butyric acid isrecycled back to the fermentation medium in the bioreactor, and themicroorganisms in the bioreactor convert the butyric acid to butanol.

In some embodiments, hydrolysis of a feedstock, e.g., lignocellulosicfeedstock, is performed with an acid, e.g., nitric acid, in multiplestages including a first stage and a second stage, the second stagehydrolysis is performed at a higher temperature than the first stage,flash steam is generated in the second stage hydrolysis, the flash steamis recompressed, and the recompressed steam is used to provide energyfor the distillation. In some embodiments, flash steam is generated inthe second stage hydrolysis, optionally recompressed, and used toprovide energy for preheating a feed stream to the distillation. In someembodiments, flash steam is generated in the second stage hydrolysis,recompressed, and used to provide energy for drying and/or dehydrationof the products separated in the distillation.

In another aspect, a system for production of a bioproduct is provided.The system includes a feedstock hydrolysis unit and a bioreactor. Acarbon-containing feedstock is hydrolyzed in the hydrolysis unit. Thehydrolyzed feedstock is continuously fed to a microbial growth medium inthe bioreactor, which contains a fermenting microorganism immobilized ona support. In some embodiments, the feedstock hydrolysis unit and thebioreactor are in fluid communication, the hydrolysis unit is upstreamfrom the bioreactor, and the feedstock is continuously hydrolyzed andcontinuously fed to the bioreactor for the duration of the fermentation.Hydrolysis of the feedstock produces carbohydrate molecules that serveas a carbon source for the fermentation, and the microorganismcontinuously converts the hydrolyzed feedstock into a bioproduct. In oneembodiment, the bioproduct is a biofuel (e.g., butanol, acetone,ethanol). In other embodiments, the bioproduct is a biochemical or abiochemical feedstock, i.e., a biochemical that may be derivatized orconverted to another product, e.g., via chemical synthesis. In someembodiments, the bioproduct is a solvent, a biomolecule, an organicacid, an alcohol, a vitamin, a fatty acid, an aldehyde, a lipid, a longchain organic molecule, or a sugar alcohol.

In some embodiments, the system contains multiple bioreactors arrangedin parallel, the multiple bioreactors are in fluid communication withthe hydrolysis unit, the hydrolyzed feedstock is fed continuously intothe bioreactors, the fermentation of the microorganism occurscontinuously in the bioreactors, and the multiple bioreactors containthe same or different microorganism(s).

In some embodiments, the system contains multiple bioreactors arrangedin series, the first bioreactor in the series is in fluid communicationwith the hydrolysis unit and with a downstream bioreactor, eachsubsequent bioreactor in the series downstream from the first bioreactoris in fluid communication with the previous upstream bioreactor in theseries, the hydrolyzed feedstock is fed continuously into the firstbioreactor in the series, and effluent from each bioreactor is fed tothe next bioreactor downstream in the series. In some embodiments,evolved gas may be removed between series nodes during operation of thebioreactors.

In one embodiment, bioreactors are arranged in parallel trains in ahybrid series/parallel arrangement. For example, fermentation mayproceed in multiple bioreactors that are arranged in a combination tooptimize productivity, such as a primary reactor arranged in series witha train of parallel reactors with hydrolyzed feedstock fed continuouslyinto the first bioreactor in the series and effluent from eachbioreactor fed to the next bioreactor downstream in the series.

In one embodiment, continuous hydrolysis and fermentation, andoptionally conditioning and/or product recovery, operate continuously inthe system for at least about 300 hours. In another embodiment,continuous hydrolysis and fermentation operate continuously in thesystem for at least about 1000 hours.

In some embodiments, the feedstock is a cellulosic material, forexample, a lignocellulosic material. In some embodiments, the feedstockis wood selected from softwood, hardwood, or a combination thereof. Insome embodiments, the feedstock is a lignocellulosic material in theform of wood chips, sawdust, saw mill residue, or a combination thereof.In some embodiments, the lignocellulosic material (e.g., wood chipssawdust, saw mill residue, or a combination thereof) is from a feedstocksource that has been subjected to some form of disease in the growthand/or harvest production period. In one embodiment, the feedstocksource is mountain pine beetle infested pine. In another embodiment, thefeedstock source is sudden oak death syndrome infested oak, e.g.,coastal live oak, tanoak, etc. In another embodiment, the feedstocksource is Dutch elm disease infested elm. In other embodiments, thefeedstock source is lignocellulosic material that has been damaged bydrought or fire.

In some embodiments, lignocellulosic feedstock material is deconstructedprior to hydrolysis. Deconstruction may include one or more processselected from presteaming, mechanical grinding, and mechanicalexplosion. In some embodiments, the feedstock material is deconstructedprior to harvest by a natural or non-natural environmental condition,for example, drought, infestation, fire, and/or herbicide exposure. Insome embodiments, the feedstock material may be deconstructed by adisease organism, for example, mountain pine beetle deconstruction ofpine.

In some embodiments, lignocellulosic feedstock material is pretreated toremove extractives. The extractive removal pretreatment may includecompression, water extraction, solvent extraction, alkaline extraction,enzymatic treatment, fungal treatment, oxygen treatment, or air drying.In some embodiments, the pretreatment to remove extractives may occurprior to or in conjunction with deconstruction.

In some embodiments, hydrolysis of a feedstock, such as alignocellulosic feedstock, is performed by treatment with an acid. Insome embodiments, the acid includes nitric acid, formic acid, aceticacid, phosphoric acid, hydrochloric acid, or sulfuric acid, or acombination thereof. In one embodiment, the hydrolysis is performed withnitric acid. In another embodiment, the hydrolysis is performed with acombination of nitric acid and acetic acid. In one embodiment, thehydrolysis is performed with nitric acid, and the hydrolysis reactorcontains stainless steel. In some embodiments, the hydrolysis reactorcontains hastelloy or zirconium. In some embodiments, hydrolysis isperformed in multiple stages in the same or different hydrolysis reactormodule(s).

In some embodiments, the hydrolysis unit contains a first hydrolysismodule and a second hydrolysis module, acid, e.g., nitric acid,hydrolysis of a feedstock, e.g., lignocellulosic feedstock, is performedin multiple stages, including a first stage in the first hydrolysismodule and a second stage in the second hydrolysis module, and thetemperature of the nitric acid in the first hydrolysis module is higherthan the temperature of the nitric acid in the second hydrolysis module.

In some embodiments, the hydrolysis product stream from the secondhydrolysis module is re-introduced into the first hydrolysis module toproduce a third hydrolysate, and the amount of soluble sugar moleculesproduced in the third hydrolysate is greater than the amount of solublesugar molecules in the second stage hydrolysate.

In some embodiments, the hydrolysis product streams from multiple, e.g.,first and second, hydrolysis modules are combined prior to introductioninto the bioreactor.

In other embodiments, the hydrolysis product streams from multiple,e.g., first and second, hydrolysis modules are introduced as separatehydrolyzed feedstock streams into separate bioreactors. For example, thefirst stage hydrolysate is introduced into a first bioreactor and thesecond stage hydrolysate is introduced into a second bioreactor, and thefirst and second bioreactors contain the same or differentmicroorganism(s). In one embodiment, the first bioreactor contains afirst microorganism and the second bioreactor contains a secondmicroorganism, the first and second microorganisms are different, andthe first microorganism is optimized for growth on the first stagehydrolysate and the second microorganism is optimized for growth on thesecond stage hydrolysate.

In some embodiments, the system contains multiple first bioreactors inseries and/or multiple second bioreactors in series.

In some embodiments, hydrolysis of a feedstock, e.g., lignocellulosicfeedstock, is performed with an acid, e.g., nitric acid, in multiplestages including a first stage and a second stage, flash steam isgenerated in the first stage hydrolysis, and the flash steam provided tothe feedstock for deconstruction of the feedstock prior to hydrolysis.In some embodiments, flash steam is generated in the second stagehydrolysis, and the flash steam is provided to the feedstock fordeconstruction of the feedstock prior to hydrolysis and/or to the firsthydrolysis module to provide energy for the first stage hydrolysis. Insome embodiments, flash steam is generated in the second stagehydrolysis, the flash steam is recompressed, and the recompressed steamis provided to the first hydrolysis module to provide energy for thefirst stage hydrolysis and/or other applications such as, for example,steam stripping distillation. In some embodiments, flash steam isgenerated in the second stage hydrolysis, the flash steam is provided toa third hydrolysis module to provide energy for a third stagehydrolysis, the temperature in the third hydrolysis module is lower thanthe temperature in the second hydrolysis module, and the lowertemperature permits hydrolysis of remaining oligomeric sugar moleculeswith less degradation than hydrolysis performed at a higher temperature.

In some embodiments, the system further includes a conditioning unitthat is in fluid communication with both the hydrolysis unit and thebioreactor, downstream from the hydrolysis unit and upstream from thebioreactor. In some embodiments, hydrolysis and conditioning processesoccur continuously for the duration of the fermentation. In oneembodiment, hydrolyzed feedstock is conditioned in the conditioning unitto remove inhibitors of microbial growth and/or production ofbioproduct—e.g., biofuel, such as butanol, prior to introduction of thehydrolyzed feedstock into the bioreactor, and the conditioning processoccurs continuously for the duration of the fermentation. In someembodiments, removal of inhibitors includes one or more process(as)selected from overliming, adsorption, precipitation, and ion exchange.In one embodiment, the conditioning unit includes an ion exchange resin,and removal of inhibitors is performed by contact of hydrolyzedfeedstock with the ion exchange resin under conditions in which theinhibitors are retained on the resin. In one embodiment, the ionexchange resin is an anion exchange resin. In one embodiment, removal ofinhibitors is performed by precipitation with a metal salt, such as analuminum or iron salt, for example, aluminum sulfate or ferric chloride.In some embodiments, the inhibitors include organic acids, furans,phenols, soluble lignocellulosic materials, extractives, and/or ketones.

In some embodiments, fermentation is conducted under anaerobicconditions. In one embodiment, the microorganism is a Clostridiumstrain.

In some embodiments, the support material on which the microorganism isimmobilized is selected from bone char, polypropylene, steel,diatomaceous earth, zeolite, ceramic, engineered thermal plastic, claybrick, concrete, lava rock, wood chips, polyester fiber, glass beads,Teflon, polyetheretherketone, and polyethylene.

In some embodiments, the immobilized microorganism includes a biofilm.

In some embodiments, the bioreactor in which the immobilizedmicroorganism is grown is in the form of a packed bed, an expanded bed,or a fluidized bed.

In some embodiments, the bioproduct is a biofuel which includes butanol,acetone, ethanol, or a combination thereof. In one embodiment, thebiofuel includes butanol.

In some embodiments, the system further includes a recovery unit forrecovery of the bioproduct from the fermentation medium. In someembodiments, the recovery unit is in fluid communication with anddownstream from the bioreactor, and the recovery process operatescontinuously for the duration of the fermentation.

In some embodiments, the recovery unit includes a concentration modulefor concentration of the bioproduct. In one embodiment, concentration ofthe bioproduct includes mechanical vapor recompression.

In some embodiments, the recovery unit includes a distillation module toseparate the bioproduct from other components of the fermentationmedium, in fluid communication with and downstream from theconcentration module. In some embodiments, flash steam generated duringhydrolysis of the feedstock provides energy for the distillation. In oneembodiment, the bioproduct is butanol, and the system contains arecovery unit for recovery of butanol from the fermentation medium.Recovery of butanol may include distillation to separate butanol fromother components of the fermentation medium. In one embodiment, butyricacid is recovered in the distillation, butyric acid is recycled back tothe bioreactor and is added to the fermentation medium in thebioreactor, and the microorganism in the bioreactor converts butyricacid to butanol.

In one embodiment, the distillation module includes a first distillationcolumn in fluid communication with and downstream from the concentrationmodule, the distillate exiting the top of the first distillation columncontains acetone and ethanol, and the distillate from the bottom of thefirst distillation column contains butanol, the distillation modulefurther includes a decanter in fluid communication with and downstreamfrom the first distillation column, the decanter comprises a top phaseand a bottom phase, and butanol and water from the top phase in thedecanter are fed into a second distillation column in fluidcommunication with and downstream from the decanter, and the distillatefrom the bottom of the second distillation column contains butanol. Inone embodiment, the distillation module further contains a thirddistillation column in fluid communication with and downstream from thefirst distillation column, distillate exiting the top of the thirddistillation column contains acetone and distillate exiting the bottomof the column comprises ethanol, and the temperature of the thirddistillation column is lower than the temperature of the firstdistillation column. In one embodiment, the distillate from the bottomof the second distillation column contains both butanol and butyricacid, and the distillation module further includes a distillation columnfor separation of butanol and butyric acid in fluid communication withand downstream from the second distillation column, distillate exitingthe top of the column for separation of butanol and butyric acidcontains butanol and distillate exiting the bottom of the columncontains butyric acid, butyric acid is recovered in the distillation,the butyric acid is provided to the fermentation medium in thebioreactor, and the microorganism converts said butyric acid to butanol.

In some embodiments, lignin is recovered in the residue of the terminalstage, e.g., second stage, of hydrolysis of lignocellulosic feedstock.In one embodiment, the lignin-containing residue is dried to a liquidcontent of about 35% to about 15%, e.g., any of about 35%, 30%, 25%,20%, or 15%, or about 35% to about 30%, about 30% to about 25%, about25% to about 20%, or about 20% to about 15% or less. In one embodiment,the lignin-containing residue is used as an energy source for saidprocess. In one embodiment, the lignin-containing residue is used as afuel source for electricity generation. In some embodiments, thelignin-containing residue is used as a chemical precursor for productionof useful products, such as phenolic resins. In some embodiments, thelignin-containing residue is used as a feed to an anaerobic digestor forproduction of useful gaseous products, such as methane or syngas. Insome embodiments, the lignin-containing residue is used as a soilenhancer.

In some embodiments, hydrolysis of a feedstock, e.g., lignocellulosicfeedstock, is performed with an acid, e.g., nitric acid, in multiplestages including a first stage and a second stage, the hydrolysis unitincludes a first hydrolysis module and a second hydrolysis module,nitric acid hydrolysis comprises a first stage in the first hydrolysismodule and a second stage in the second hydrolysis module, thetemperature of the nitric acid in the first hydrolysis module is higherthan the temperature of the nitric acid in the second hydrolysis module,flash steam is generated in the second stage hydrolysis, the flash steamis recompressed, and the recompressed steam is used to provide energyfor said distillation. In some embodiments, flash steam is generated inthe second stage hydrolysis, optionally recompressed, and used toprovide energy for preheating a feed stream to said distillation. Insome embodiments, flash steam is generated in the second stagehydrolysis, the flash steam is recompressed, and the recompressed steamis used to provide energy for drying and/or dehydration of the productsseparated in the distillation.

In some embodiments, an extractives stream removed before or duringfeedstock hydrolysis and/or flash steam generated during feedstockhydrolysis is in fluid communication with the product recovery system inorder to recover additional products of value, such as terpenes,sterols, sterol esters, resin acids, fatty acids, wax esters,diglycerides, triglycerides, and/or methanol. In some embodiments, flashsteam generated during feedstock hydrolysis is in fluid communicationwith the product recovery system for use as a distillation aid, forpreheating the feed mixture and/or for use in steam strippingdistillation.

In some embodiments, material recovered from a primary product recoverycolumn, from which a bioproduct, e.g., a solvent, has been removed, isreintroduced into the bioproduct production system. For example, thematerial may used as primary dilution water or rinse water (for example,to rinse sugars from biomass), or other water addition stream. In sodoing, fermentation nutrients may be reintroduced to the process,reducing cost and/or increasing performance, sugars may be reintroducedto the process, improving process yield, and/or water may be reused.

In some embodiments of the bioproduct production processes and systemsherein, the bioreactor(s) operated under pressure to compress gas in thebioreactor(s), for example, CO₂ generated by the microorganisms duringfermentation.

INCORPORATION BY REFERENCE

All publications, patents, and patent applications mentioned in thisspecification are herein incorporated by reference to the same extent asif each individual publication, patent, or patent application wasspecifically and individually indicated to be incorporated by reference.

BRIEF DESCRIPTION OF THE DRAWINGS

The novel features of the invention are set forth with particularity inthe appended claims. A better understanding of the features andadvantages of the present invention will be obtained by reference to thefollowing detailed description that sets forth illustrative embodiments,in which the principles of the invention are utilized, and theaccompanying drawings of which:

FIG. 1 shows a schematic diagram of an embodiment of an integratedbiofuel plant in which biobutanol production processes and systemsdescribed herein may be utilized.

FIG. 2 shows a schematic diagram of an embodiment of an integratedbiofuel plant in which biobutanol production processes and systemsdescribed herein

FIG. 3 shows a process flow diagram for an embodiment of an integratedbiofuel plant in which biofuel production processes and systemsdescribed herein may be utilized.

FIG. 4 shows a schematic diagram of an embodiment of a two-stagefeedstock hydrolysis process.

FIG. 5 shows the results of HPLC analysis of effluent from microbialfermentation on conditioned and unconditioned hydrolyzed feedstock, asdescribed in Example 4.

FIG. 6 shows the results of continuous culture of immobilizedClostridium, in run no. 2008065 (strain Co-7449 on 4% glucose) asdescribed in Example 1.

FIG. 7 shows the results of continuous culture of immobilizedClostridium, in run no. 2009012 (strain Co-5673 on 5% sucrose) asdescribed in Example 1.

FIG. 8 shows the results of continuous culture of immobilizedClostridium, in run no. 2009021 (strain Co-7449 on 4% xylose) asdescribed in Example 1.

FIG. 9 shows the results of continuous culture of immobilizedClostridium, in run no. 2009023 (strain Co-5673 on 4% xylose) asdescribed in Example 1.

FIG. 10 shows the results of continuous culture of immobilizedClostridium, in run no. 2009057 (strain Co-5673 on 4% mixed sugarsimulated hydrolysate) as described in Example 1.

FIG. 11 shows the results of continuous culture of immobilizedClostridium, in run no. 2008137 (strain Co-5673 on 4% mixed sugarsimulated hydrolysate) as described in Example 1.

FIG. 12 shows the results of continuous culture of immobilizedClostridium, in run no. 2009060 (strain Co-7449 on 4% sucrose) asdescribed in Example 1.

FIG. 13 shows the residual material remaining after performing thehemicellulose extraction procedure described in Example 7 with acid(right hand panel) or water (left hand panel).

DETAILED DESCRIPTION OF THE INVENTION

The invention provides processes and systems for continuous bioproduct,e.g., biofuel, production via microbial fermentation. In the processesand systems described herein, microbial fermentation is utilized toconvert sugars extracted from a carbohydrate-containing feedstock toproduce a bioproduct, such as a biofuel, for example, biobutanol andoptionally other co-products.

Unless defined otherwise herein, all technical and scientific terms usedherein have the same meaning as commonly understood by one of ordinaryskill in the art to which this invention belongs. Singleton, et al.,Dictionary of Microbiology and Molecular Biology, second ed., John Wileyand Sons, New York (1994), and Hale & Markham, The Harper CollinsDictionary of Biology, Harper Perennial, NY (1991) provide one of skillwith a general dictionary of many of the terms used in this invention.Any methods and materials similar or equivalent to those describedherein can be used in the practice or testing of the present invention.

Numeric ranges provided herein are inclusive of the numbers defining therange.

DEFINITIONS

“A,” “an” and “the” include plural references unless the context clearlydictates otherwise.

“Bioproduct” refers to any substance of interest produced biologically,i.e., via a metabolic pathway, by a microorganism, e.g., in a microbialfermentation process. Bioproducts include, but are not limited tobiofuels (e.g., butanol, acetone, ethanol), solvents, biomolecules(e.g., proteins (e.g., enzymes), polysaccharides), organic acids (e.g.,formate, acetate, butyrate, propionate, succinate, lactate, adipic acid,amino acids), alcohols (e.g., methanol, propanol, isopropanol, pentanol,hexanol, 2-butanol, isobutanol, glycerol), fatty acids, aldehydes (e.g.,acetaldehyde, butyraldehyde), ketones (e.g., butanone), lipids, longchain organic molecules (for example, for use in surfactant production),vitamins, and sugar alcohols (e.g., xylitol).

“Biofuel” refers to fuel molecules (e.g., butanol, acetone, and/orethanol) produced biologically by a microorganism, e.g., in a microbialfermentation process.

“Biobutanol” refers to butanol (i.e., n-butanol) produced biologicallyby a microorganism, e.g., in a microbial fermentation process.

“Byproduct” refers to a substance that is produced and/or purifiedand/or isolated during any of the processes described herein, which mayhave economic or environmental value, but that is not the primaryprocess objective. Nonlimiting examples of byproducts of the processesdescribed herein include lignin compounds and derivatives, carbohydratesand carbohydrate degradation products (e.g., furfural, hydroxymethylfurfural, formic acid), and extractives (described infra).

“Feedstock” refers to a substance that can serve as a source of sugarmolecules to support microbial growth in a fermentation process. In someembodiments, the feedstock must be pretreated to release the sugarmolecules. In one embodiment, the feedstock, which contains carbohydratepolymers, is hydrolyzed to release 5 and/or 6 carbon containingcarbohydrate molecules in monomeric and/or soluble oligomeric forms.

“Deconstruction” refers to mechanical, chemical, and/or biologicaldegradation of biomass into to render individual components (e.g.,cellulose, hemicellulose) more accessible to further pretreatmentprocesses, for example, a process to release monomeric and oligomericsugar molecules, such as acid hydrolysis.

“Conditioning” refers to removal of inhibitors of microbial growthand/or bioproduct, e.g., biofuel, production from a feedstock orpretreated feedstock (e.g., a hydrolysate produced by hydrolysis of afeedstock) and/or adjustments to physical properties of the feedstock orpretreated feedstock to improve conditions that support microbial growthand product production.

“Titer” refers to amount of a substance produced by a microorganism perunit volume in a microbial fermentation process. For example, biobutanoltiter may be expressed as grams of butanol produced per liter ofsolution.

“Yield” refers to amount of a product produced from a feed material (forexample, sugar) relative to the total amount that of the substance thatwould be produced if all of the feed substance were converted toproduct. For example, biobutanol yield may be expressed as % ofbiobutanol produced relative to a theoretical yield if 100% of the feedsubstance (for example, sugar) were converted to biobutanol.

“Productivity” refers to the amount of a substance produced by amicroorganism per unit volume per unit time in a microbial fermentationprocess. For example, biobutanol productivity may be expressed as gramsof butanol produced per liter of solution per hour.

“Wild-type” refers to a microorganism as it occurs in nature.

“Biomass” refers to cellulose- and/or starch-containing raw materials,including but not limited to wood chips, corn stover, rice, grasses,forages, perrie-grass, potatoes, tubers, roots, whole ground corn, grapepomace, cobs, grains, wheat, barley, rye, milo, brans, cereals,sugar-containing raw materials (e.g., molasses, fruit materials, sugarcane, or sugar beets), wood, and plant residues.

“Starch” refers to any starch-containing materials. In particular, theterm refers to various plant-based materials, including but not limitedto wheat, barley, potato, sweet potato, tapioca, corn, maize, cassava,milo, rye, and brans. In general, the term refers to any materialcomprised of the complex polysaccharide carbohydrates of plants,comprised of amylose, and amylopectin, with the formula (C₆H₁₀O5)_(x),wherein “x” can be any number.

“ABE fermentation” refers to production of acetone, butanol, and/orethanol by a fermenting microorganism.

“Advanced biofuels” are high-energy liquid transportation fuels derivedfrom low nutrient input/high per acre yield crops, agricultural orforestry waste, or other sustainable biomass feedstocks including algae.

“Lignocellulosic” biomass refers to plant biomass that containscellulose, hemicelluloses, and lignin. The carbohydrate polymers(cellulose and hemicelluloses) are tightly bound to lignin.

“Lignins” are macromolecular components of wood that contain phenolicpropylbenzene skeletal units linked at various sites.

n-Butanol (1-butanol) is also referred to as “butanol” herein.

“ATCC” refers to the American Type Culture Collection, P.O. Box 1549,Manassas, Va. 20108.

Feedstock

A feedstock is a substance that provides the base material from whichsugar molecules are generated for inclusion in a microbial growthmedium, to support the growth of the microorganism. In some embodiments,the feedstock is cellulosic biomass. In some embodiments, the feedstockcontains cellulose and hemicellulose, for example, lignocellulosicbiomass or wood pulp. In some embodiments, the feedstock is apolysaccharide from which soluble sugar molecules may be produced thatcan support growth of a microorganism, for example, a polysaccharidewaste product such as crab, shrimp, or lobster shells, chitin, chitosan,pectin, or sucrose.

In some embodiments, the feedstock is woody biomass. In one embodiment,the feedstock is softwood, for example, pine, e.g., Lodgepole orLoblolly pine. In one embodiment, the feedstock contains mountain pinebeetle infested pine, for example, dying (“red stage”) or dead (“grey”stage). In another embodiment, the feedstock is hardwood, for example,maple, birch, or ash. In another embodiment, the feedstock is mixedhardwood and softwood. In another embodiment, the feedstock is mixedhardwood. In some embodiments, the woody biomass is in the form of woodchips, sawdust, saw mill residue, wood fines, or a combination thereof.

In some embodiments, the feedstock is obtained as a process stream froma biomass processing facility, for example, a pulp mill. In variousembodiments of pulp mill process streams, the process stream may includereject pulp, wood knots or shives, pulp screening room rejects (e.g.,essentially cellulose in water), prehydrolysis extraction stream, and/orblack liquor. In other embodiments, the feedstock may include bagasse,corn cobs, beet molasses, pulp and/or paper, sweet sorghum syrup, orbarley hulls.

Lignocellulose contains a mixture of carbohydrate polymers andnon-carbohydrate compounds. The carbohydrate polymers contain celluloseand hemicellulose, and the non-carbohydrate portion contains lignin. Thenon-carbohydrate portion may also contain ash, extractives, and/or othercomponents. The specific amounts of cellulose, hemicelluloses, andlignin depends on the source of the biomass. For example, municipalsolid waste may contain primarily cellulose, and extract streams from apaper and pulp plant may contain primarily hemicelluloses. The remainingcomposition of lignocellulose may also contain other compounds such asproteins.

Cellulose, which is a β-glucan built up of D-glucose units linked byβ(1,4)-glycosidic bonds, is the main structural component of plant cellwalls and typically constitutes about 35-60% by weight (% w/w) oflignocellulosic materials.

Hemicellulose refers to non-cellulosic polysaccharides associated withcellulose in plant tissues. Hemicellulose frequently constitutes about20-35% w/w of lignocellulosic materials, and the majority ofhemicelluloses consist of polymers based on pentose (five-carbon) sugarunits, such as D-xylose and D-arabinose units, hexose (six-carbon) sugarunits, such as D-glucose and D-mannose units, and uronic acids such asD-glucuronic acid.

Lignin, which is a complex, cross-linked polymer based on variouslysubstituted p-hydroxyphenylpropane units, typically constitutes about10-30% w/w of lignocellulosic materials.

Any material containing cellulose and/or hemicellulose or celluloseand/or hemicellulose oligomeric and/or monomeric compounds (e.g., sugarmonomers, dimers (e.g., cellobiose), trimers (e.g., cellotriose)) may beused as the feedstock. The material may contain cellulose and/orhemicellulose without lignin.

Lignocellulosic biomass may be derived from a fibrous biologicalmaterial such as wood or fibrous plants. Examples of suitable types ofwood include, but are not limited to, spruce, pine, hemlock, fir, birch,aspen, maple, poplar, alder, salix, cottonwood, rubber tree, marantii,eucalyptus, sugi, and acase. Examples of suitable fibrous plantsinclude, but are not limited to, corn stover and fiber, flax, hemp,cannabis, sisal hemp, bagasse, straw, cereal straws, reed, bamboo,mischantus, kenaf, canary reed, Phalaris arundinacea, and grasses. Otherlignocellulosic materials may be used such as herbaceous material,agricultural crop or plant residue, forestry residue, municipal solidwaste, pulp or paper mill residue, waste paper, recycling paper, orconstruction debris. Examples of suitable plant residues include, butare not limited to, stems, leaves, hulls, husks, cobs, branches,bagasse, wood chips, wood pulp, wood pulp, and sawdust. Examples ofsuitable waste paper include, but are not limited to, discarded paper ofany type (e.g., photocopy paper, computer printer paper, notebook paper,notepad paper, typewriter paper), newspaper, magazines, cardboard, andpaper-based packaging material. Materials with high mineral content maypotentially require additional pH adjustment (e.g., additional amountsof chemicals for pH adjustment) for effective processing.

In embodiments in which wood is used as the feedstock, the bioproduct,e.g., biofuel, production plant can include a facility to unload, washand screen incoming wood chips to remove any dirt and debris. The chipscan be ground to the optimum size for hydrolysis and conveyed to thefeed hopper for introduction into the hydrolysis unit. Data can becollected from a feedstock provider and used to size and specify thewood handling equipment for a given plant.

Other feedstocks that may be used in the bioproduct (e.g., biofuel, forexample, biobutanol) production processes described herein includehemicellulose extract from wood, beet extract, beet molasses, sorghumsyrup, barley hulls, potato processing waste, and brewers mash.

In some embodiments, a feedstock mix containing about 40% loggingresidues, about 20% sustainable roundwood, about 20% woody energy crops,and about 20% herbaceous energy crops may be used. This blend canaccount for regional variation and provide significant flexibility inselecting locations for facilities and in procuring feedstock supplycontracts.

Feedstock flexibility may permit utilization of combinations offeedstocks in geographic locations where the available supply offeedstocks taken individually are not sufficient to justify a commercialscale bioproduct, e.g., biobutanol, production plant, or wheresynergistic value can be realized from combining feedstocks that allowfor better practices to be implemented with regard to the underlyingland (e.g, improved crop rotations) or in terms of more economicharvest, handling and storage logistics. Feedstock flexibility may alsoprovide opportunities to locate plants in niche sites where end usemarkets are in close proximity to otherwise non-utilizable feedstocks.

In some embodiments, diverse feedstocks may be utilized by versatilestrains which are capable of converting both 5-carbon and 6-carbon sugarmolecules (including multimeric forms) to a bioproduct, e.g., biofuel,for example, n-butanol. In some embodiments, a feedstock may behydrolyzed to provide hydrolysates that are rich in 5-carbon or 6-carbonsugars, and microbial strains which have been optimized for growth andbioproduct, e.g., biofuel, production on 5-carbon or 6-carbon sugars areused for bioproduct production, either in separate or combinedfermentations. In some embodiments, a microbial strain that has beenoptimized for growth on a particular feedstock or hydrolysate generatedfrom a particular feedstock, is used for bioproduct, e.g., biofuel,production.

Pretreatment of Feedstock

Feedstocks such as those described herein can be pretreated using avariety of methods and systems prior to bioconversion. Preparation ofthe feedstock can include chemical or physical modification of thefeedstock. For example, the feedstock can be shredded, sliced, chipped,chopped, heated, burned, dried, separated, extracted, hydrolyzed, and/ordegraded. These modifications can be performed by biological,non-biological, chemical, or non-chemical processes.

In some embodiments in which a cellulosic, e.g., lignocellulosic,feedstock is used, processes may be used to break down cellulose and/orhemicellulose into sugar molecules that may be more easily processed bya microorganism. Processes that may be used include acid hydrolysis,enzymatic hydrolysis, gasification, pyrolysis, and cellulose degradationby a microorganism.

Deconstruction

In some embodiments, the feedstock, such as lignocellulosic feedstock,for example, wood chips, sawdust, and/or sawdust residue, isdeconstructed prior to a downstream pretreatment process such ashydrolysis. Deconstruction may include, but is not limited to,presteaming to swell and loosen material, mechanical grinding,mechanical explosion (e.g., steam or other chemical treatment followedby rapid decompression), vacuum treatment, acid-feedstock contact(diffusion of acid into feedstock), or a combination thereof. In someembodiments, deconstruction renders cellulose and/or hemicellulose inthe feedstock more accessible for hydrolysis.

Removal of Extractives

In some embodiments, the feedstock, such as lignocellulosic feedstock,for example, wood chips, sawdust, and/or sawdust residue, is pretreatedto remove extractives. Extractives are material that is extracted fromthe feedstock by a process such as compression, water or solventextraction, or air drying. Non-limiting examples of extractives includeterpenes, resin acids, fatty acids, sterols, phenolic compounds, andtriglycerides. Extractives may include, but are not limited to,p-coumaric acid, ferulic acid, 4-hydroxybenzoic acid, vanillic acid,syringaldehyde, vanillin, furfural, hydroxymethylfurfural, andglucuronic acid. Extractives may be removed for other uses, such asproduction of sterols, or burned to provide energy for a bioproduct,e.g., biofuel, production process as described herein.

In some embodiments, extractives are removed prior to or in conjunctionwith deconstruction of the feedstock.

Hydrolysis

Typically, a feedstock contains sugar molecules in an oligomeric form,e.g., a polymeric form, and must be hydrolyzed to extract and releasesoluble monomeric and/or multimeric sugar molecules, which are convertedto bioproduct, e.g., biofuel, in a microbial fermentation as describedherein. In some embodiments, the sugar molecules are present in thefeedstock in cellulose and/or hemicellulose. In one embodiment, thefeedstock is lignocellulosic biomass and the sugar molecules are presentin the feedstock in cellulose and hemicellulose.

In some embodiments, the feedstock is pretreated with an acid hydrolysisprocess. Acids that may be used for hydrolysis include, but are notlimited to, nitric acid, formic acid, acetic acid, phosphoric acid,hydrochloric acid, and sulfuric acid, or a combination thereof. In oneembodiment, acid hydrolysis is performed in a single stage. In someembodiments, acid hydrolysis is performed in two or more stages, underdifferent conditions in each stage to hydrolyze different components ofthe feedstock in each stage. Acid hydrolysis performed in multiplestages may serve to limit the impact of kinetically controlledcarbohydrate degradation mechanisms. A schematic diagram of anembodiment of a two-stage acid hydrolysis process is depicted in FIG. 4.

An acid hydrolysis system may be designed to submerge and flood thefeedstock with the acid solution in the hydrolysis reactor, e.g., in avertical section of the hydrolysis reactor, to insure even acidimpregnation. Even heat distribution may be obtained by using bothdirect steam injection and a jacketed vessel in conjunction with amechanical screw auger. Variable speed drives may be used withtemperature sensing instrumentation to control reactor residence timeand temperature allowing reactor severity to be adjusted on-line.Alternative reactor configurations with functionally similar propertiesmay also be utilized. For example, a horizontal digestor configurationmay be used. In this type of reactor, the material is only partiallysubmerged. Similarly, in some embodiments, in order to reach highersoluble sugar concentrations, the feedstock material is not completelysubmerged in the acid containing solution, thereby producing ahydrolysate that contains an increased sugar concentration (i.e., lessdilution water added at the outset). In some embodiments, amultiple-stage dilute nitric acid hydrolysis process is used. In oneembodiment, a two-stage dilute nitric acid process is used. In oneembodiment, conditions in the first stage are chosen to achievehydrolysis of about 70% to about 90% of the hemicellulose in thefeedstock and conditions in the second stage are chosen to achievehydrolysis of about 40% to about 70% of the cellulose in the feedstock.The first stage mainly targets the hydrolysis of the hemicellulose,yielding a mannose and/or xylose rich hydrolysate, whereas the secondstage uses the solids remaining from the first stage and targets thecellulose, yielding a glucose rich hydrolysate. Typically, first stagehydrolysate liquors contain a mix of 5-carbon and 6-carbon sugars, e.g.,extracted primarily from hemicellulose and non-recalcitrant cellulosebiomass components, and second stage hydrolysate contains primarily6-carbon sugars, e.g., extracted from cellulose fibers, in both cases assoluble monomeric and/or multimeric forms. 6-carbon monosaccharides mayinclude, but are not limited to, glucose, mannose, and galactose.6-carbon disaccharides may include, but are not limited to, cellobiose,mannobiose, glucomannose, and galactomannose. Other multimeric forms mayinclude, but are not limited to, cellotriose, cellotetrose, andcellopentose. 5-carbon monosaccharides may include, but are not limitedto xylose and arabinose. 5-carbon disaccharides and other multimericforms may include, but are not limited to, xylobiose, xylotriose, andarabinoxylose.

In some embodiments in which hardwood is used as the feedstock, thefirst stage hydrolysate contains about 60% to about 75% 5-carbon sugarby weight and about 25% to about 40% 6-carbon sugar by weight, and thesecond stage hydrolysate contains about 80% to about 95% 6-carbon sugarby weight. In some embodiments in which softwood is used as thefeedstock, the first stage hydrolysate contains about 20% to about 30%5-carbon sugar by weight and about 70% to about 80% 6-carbon sugar byweight, and the second stage hydrolysate contains about 90% to about100% 6-carbon sugar by weight, wherein the second stage is performed ata higher temperature than the first stage.

A first stage hydrolysis module may be coupled to a second stagehydrolysis module, with solid residue separated from liquid hydrolysategenerated in the first stage hydrolysis serving as substrate for thesecond hydrolysis process. The residual solids may be rinsed/washed inorder to increase the separation and recovery yield of soluble sugarsseparated from the biomass.

In some embodiments, the second stage hydrolysis is performed at ahigher temperature than the first stage hydrolysis.

In some embodiments, hydrolysis is performed at a nitric acidconcentration of about 0.05 to about 0.1%, about 0.1% to about 0.5%,about 0.5% to about 1%, about 1% to about 4%, about 1.3% to about 3.5%,or about 1.3% (w/w of dry feedstock) for both hydrolysis stages, at atemperature of about 170° to about 175° C. in the first stage and atemperature of about 210° to about 230° C. in the second stage, and atthe saturation pressure for steam at the reactor temperature for eachhydrolysis stage.

In some embodiments, the liquid (acid) to solid (feedstock) ratio forhydrolysis is about 10:1 to about 5:1 or about 7.5:1 to about 5:1. In acirculating reactor, the ratio of liquid to solid may be about 5:1 toabout 3:1 or about 3.5:1 to about 3:1. In a continuous extrusionreactor, the ratio of liquid to solid may be about 4:1 to about 0.5:1.

In some embodiments, the soluble sugar extraction yield from thefeedstock in the first stage hydrolysis as about or at least about 6,10, 15, 20, 30, 34, 40, 50, or 60% from cellulose and about or at leastabout 1, 3, 6, 10, 20, 40, 60, 70, 75, 80, 85, 90, 95, or 99% fromhemicellulose. In some embodiments, the soluble sugar extraction yieldfrom solid residue remaining after the first stage hydrolysate in thesecond stage hydrolysis is about or at least about 25, 35, 45, 55, 65,75, 85, or 95% from cellulose and about or at least about 1, 3, 6, or10% from hemicellulose. In some embodiments, conditions are chosen suchthat short residence times may be utilized, providing high productivity(smaller reactors) and minimal sugar degradation products. Minimizingdegradation products makes the pretreatment step more compatible withthe downstream fermentation process. For example, in some embodiments,residence time in the hydrolysis reactor for first stage nitric acidhydrolysis with ¼ inch wood chips may be about 5 to about 8 minutes,with longer residence time of about 3 to about 15, or up to about 30minutes for larger feed material, and residence time for ¼ inch woodchips for second stage nitric acid hydrolysis may be about 3 to about 6minutes, or about 3 to about 20 minutes, with longer residence time forlarger feed material. The residence times may be affected by the degreeof material deconstruction and/or the applied acid conditions.

Dilute nitric acid pretreatment has several advantages over other typesof acid pretreatment. The passivation characteristics of nitric acid atlignocellulosic pretreatment conditions permit the use of stainlesssteel, rather than the more exotic and expensive materials required forother pretreatment processes, such as dilute sulfuric acid treatment.This confers a substantial capital cost advantage. Further, thehydrolysis and neutralization process is rich in nitrogen that can beutilized in fermentation. In some embodiments, hydrolysate streams areneutralized with ammonia to produce ammonium nitrate Ammonium nitrate isa nutrient for microorganisms in the downstream fermentation process.

Parameters for nitric acid hydrolysis of feedstock are also described inU.S. Pat. Nos. 4,384,897, 4,706,903, 5,221,357, 5,366,558, 5,536,325,5,628,830, and 6,019,900.

In a multiple-stage hydrolysis process as described herein, hydrolysisreactors for each stage may be the same or different. For example, asecond stage reactor may have a higher or lower capacity than a firststage reactor. In some embodiments, a hydrolysis reactor may have aninternal volume of about or at least about 1, 2, 5, 10, 20, 50, 100,200, 500, 1000, 2500, 5000, 10,000, 50,000, 100,000, 150,000, or 200,000gallons. In some embodiments, a nitric acid hydrolysis reactor may besmaller than a comparable capacity sulfuric acid hydrolysis reactor.

In a multiple-stage hydrolysis process as described herein, such as atwo-stage nitric acid hydrolysis process, one or more processingoperations can be used between stages, such as between first and secondnitric acid hydrolysis stages, including mechanical degradation, drying,shaking, mixing, chipping, straining, solid-liquid, liquid-liquid, orgas-liquid separation phase separation, decanting, and shearing. Suchoperations may be used for separation, degradation, attrition, orshearing of an input material.

In some embodiments, a hydrolysis system can include a steam compressorto compress low pressure flash steam. In some embodiments, low pressureflash steam from the first and/or second stage of a nitric acidhydrolysis process may be compressed. By raising the pressure, the lowpressure flash steam can be reused in downstream product concentrationand/or product distillation operations and significantly reduce theenergy requirements of the overall process. In other embodiments, flashsteam may be used productively in steam stripping distillation,permitting recovery of useful products contained in the flash stream.

A hydrolysis system for use in the processes described herein can beoptimized to produce the greatest yield of products per amount offeedstock, energy required, greenhouse gas emitted, or any combinationthereof. Optimization parameters include the type of separations orreactions performed outside of the hydrolysis reactors, and theconditions of the hydrolysis reactors. In some embodiments, degradationand/or hydrolysis of the feedstock material may be reduced or increaseddue to impact on energy consumption or product yield.

In bioproduct, e.g., biofuel, production processes and systems describedherein, a feedstock hydrolysis process as described herein and afermentation process are coupled to process feedstock in a continuousmanner. The continuous operation may be designed such that accumulationof materials between the hydrolysis unit and fermentor is avoided. Insome embodiments, a hydrolysis unit may be operated continuously forabout or at least about 50, 100, 200, 300, 400, 600, 800, 1000, 1350,1600, 2000, 2500, 3000, 4000, 5000, 6000, or 8500 hours.

Lignin-containing residue remaining after hydrolysis of alignocellulosic feedstock may be used as an energy source for thebioproduct, e.g., biofuel, production process described herein and/or asa fuel source for electricity generation. In some embodiments,lignin-containing residue is dried to a liquid content of about 35% toabout 15%, e.g., any of about 35%, 30%, 25%, 20%, or 15%, or about 35%to about 30%, about 30% to about 25%, about 25% to about 20%, or about20% to about 15% or less and the dried residue may be burned as a fuelsource for energy or electricity generation, gasified for subsequentcombustion or conversion to other chemical products, or converted toother chemical products.

In one embodiment, a method is provided for deconstructing biomass thatcontains cellulose and hemicellulose for the extraction of sugarmolecules from the biomass. The method includes: (a) mechanicallydisintegrating the biomass in the presence of water and under pressure,thereby producing liquid and/or vapor and solid disintegrated biomass;(b) separating liquid and/or vapor from the biomass, wherein step (b)may be performed after or in conjunction with step (a); (c) contactingthe disintegrated biomass with acid in an amount sufficient todepolymerize a polymeric carbohydrate component of the biomass, therebyproducing acid impregnated disintegrated biomass; (d) feeding the acidimpregnated disintegrated biomass into a digestor through a pressurechanging device, wherein the acid impregnated disintegrated biomass isheated in the digestor at a temperature and for an amount of timesufficient to permit the depolymerization reaction to occur; and (e)separating solids from liquids to produce a liquid hydrolysate andresidual solids, wherein the hydrolysate contains soluble hemicellulosesugar molecules and the residual solids contain cellulosic fiber, forexample, fiber that is at least about 0.35 or 0.37 mm in length. In someembodiments, the acid is nitric acid at a concentration of about 0.1%(w/w) to about 0.5% (w/w). In some embodiments, the digestor is operatedat a pressure of about 90 to about 110 psig, a temperature of about 167°C. to about 176° C. and a residence time of about 3 to about 20, about 8to about 20, or about 5 to about 10 minutes. In some embodiments, thebiomass is contacted with steam prior to acid impregnation, which mayaid with disintegration of the biomass and extractives removal. In someembodiments, the residual solids are further hydrolyzed, for example, byacid hydrolysis, to release soluble sugar molecules from the cellulosefiber, thereby producing a further hydrolysate that may be used tosupport microbial fermentation in the processes and systems describedherein.

In another embodiment, the method described above for deconstructingbiomass that contains cellulose and hemicellulose for the extraction ofsugar molecules from the biomass is performed with an acid concentrationin step (c), a residence time in step (d), and a temperature in step (d)sufficient to produce a hydrolysate that contains hemicellulose sugarsand residual solids that contain cellulosic fiber that is less thanabout 0.35, 0.30, or 0.28 mm in length. In one embodiment, the residualsolids do not contain visible cellulosic fiber. In some embodiments, theacid concentration in step (c) is about 1% (w/w) to about 1.5% (w/w),the residence time in step (d) is about 5 minutes to about 10 minutes,and the temperature in step (d) is about 160° C. to about 180° C. Insome embodiments, the acid is nitric acid at a concentration of about0.05% (w/w) to about 4% (w/w). In some embodiments, the digestor isoperated at a pressure of about 90 to about 110 psig, a temperature ofabout 160° C. to about 180° C., and a residence time of about 4 to about15 min. In some embodiments, the biomass is contacted with steam priorto acid impregnation, which may aid with disintegration of the biomassand extractives removal. In some embodiments, the residual solids arefurther hydrolyzed, for example by acid or enzymatic hydrolysis, therebyproducing a further hydrolysate that may be used to support microbialfermentation in the processes and systems described herein.

In another embodiment, a method is provided for deconstructing biomassthat contains cellulose and hemicellulose for the extraction of sugarmolecules from the biomass, including: (a) contacting the biomass withacid in an amount sufficient to depolymerize a polymeric carbohydratecomponent of the biomass, thereby producing acid impregnateddisintegrated biomass; (b) feeding the acid impregnated disintegratedbiomass into a digestor through a pressure changing device, wherein theacid impregnated disintegrated biomass is heated in said digestor at atemperature and for an amount of time sufficient to permit thedepolymerization reaction to occur; and (c) separating solids fromliquids to produce a liquid hydrolysate and residual solids, wherein thehydrolysate comprises hemicellulose sugar molecules and the residualsolids contain fiber that is less than about 0.35, 0.30, or 0.28 mm inlength. In one embodiment, the residual solids do not contain visiblecellulosic fiber. In some embodiments, the acid is nitric acid at aconcentration in step (a) is about 0.1% (w/w) to about 5% (w/w), orabout 1% (w/w) to about 3% (w/w), the residence time in step (b) isabout 8 to about 20 minutes, and the temperature in step (b) is about160° C. to about 180° C. In some embodiments, the biomass is contactedwith steam prior to acid impregnation, which may aid with disintegrationof the biomass and extractives removal. In some embodiments, theresidual solids are further hydrolyzed, for example by acid or enzymatichydrolysis, thereby producing a further hydrolysate that may be used tosupport microbial fermentation in the processes and systems describedherein.

Conditioning of Hydrolyzed Feedstock

In some embodiments, hydrolyzed feedstock is “conditioned” to removeinhibitors of microbial growth and/or bioproduct, e.g, biofuel,production, prior to addition of the hydrolyzed feedstock to microbialgrowth medium. Such inhibitors may include, but are not limited to,organic acids, furans, phenols, soluble lignocellulosic materials,extractives, and ketones Inhibitors present in wood hydrolysates mayinclude, but are not limited to, 5-hydroxyy-methyl furfural (HMF),furfural, aliphatic acids, levulinic acid, acetic acid, formic acid,phenolic compounds, vanillin, dihydroconiferylalcohol, coniferylaldehyde, vanillic acid, hydroquinone, catechol, acetoguaiacone,homovanillic acid, 4-hydroxy-benzoic acid, Hibbert's ketones, ammoniumnitrate and/or other salts, p-coumaric acid, ferulic acid,4-hydroxybenzoic acid, vanillic acid, syringaldehyde, and glucuronicacid.

Nonlimiting examples of conditioning processes include vacuum or thermalevaporation, overliming, precipitation, adsorption, enzymaticconditioning (e.g., peroxidase, laccase), chemical conversion,distillation, and ion exchange. In one embodiment, conditioning includescontact of hydrolyzed feedstock with an ion exchange resin, such as ananion or cation exchange resin. Inhibitors may be retained on the resin.In one embodiment, the ion exchange resin is an anion exchange resin.Ion exchange resins may be regenerated with caustic, some solvents,potentially including those generated in the bioproduct, e.g., biofuel,production processes described herein, or other known industrialmaterials. In other embodiments, inhibitors may be precipitated by ametal salt (for example, a trivalent metal salt, for example, analuminum or iron salt, such as aluminum sulfate or ferric chloride),and/or a flocculant such as polyethylene oxide or other low density,high molecular weight polymers.

In one embodiment, hydrolysate is conditioned on ion exchange resin,such as an anion exchange resin, e.g., Duolite A7, at acidic pH, forexample, pH about 2.5 to about 5.5, about 3.5 to about 4.5, or about2.5, 3, 3.5, 4, 4.5, 5, or 5.5.

In one embodiment, hydrolysate is conditioned with a metal salt, forexample, a trivalent metal salt, such as an aluminum or iron salt, e.g.,aluminum sulfate or ferric chloride. In some embodiments, the metal saltis added at a concentration of about 1 g/L to about 6 g/L, or about 3g/L to about 5 g/L. In some embodiments, the pH is adjusted with a baseto a basic pH, such as about 9.5 to about 11, or about 9.5, 10, 10.5, or11, for example, with ammonium hydroxide or ammonia gas.

In some embodiments, microbial growth and/or bioproduct, e.g., biofuel,titer, yield, and/or productivity is increased when conditionedhydrolyzed feedstock is used, in comparison to identical hydrolyzedfeedstock which has not been subjected to the conditioning process.

In some embodiments, a microorganism that is tolerant to inhibitors inhydrolyzed feedstock is used, or the microorganism used for bioproductproduction develops increased tolerance to inhibitors over time, e.g.,by repeated passaging, rendering the conditioning step unnecessary oruneconomical.

In one embodiment, an extractive removal process, as described supra, isused instead of a conditioning process to improved microbial growthand/or bioproduct, e.g., biofuel, titer, yield, and/or productivity. Inone embodiment, an extractive removal process, as described supra, isused in addition to a conditioning process to improve microbial growthand/or bioproduct, e.g., biofuel, titer, yield, and/or productivity. Anextractive removal process may also be used in some embodiments togenerate an additional stream to provide products with commercial value(e.g., sterols) and/or to improve operational parameters (e.g., lessresin and regenerant to regenerate the resin (e.g., caustic) requiredfor removal of fermentation and/or bioproduct, e.g., biofuel, productioninhibitors.

Fermentation

The bioproduct production process herein includes fermentation of amicroorganism that produces a bioproduct, e.g., a biofuel, in animmobilized cell bioreactor (i.e., a bioreactor containing cells thatare immobilized on a support, e.g., a solid support). In someembodiments, an immobilized cell bioreactor provides higher productivitydue to the accumulation of increased productive cell mass within thebioreactor compared with a stirred tank (suspended cell) bioreactor. Insome embodiments, the microbial cells form a biofilm on the supportand/or between support particles in the growth medium.

The bioproduct, e.g., biofuel, production process herein includescontinuous fermentation of a microorganism (continuous addition offeedstock (e.g., hydrolyzed feedstock) and withdrawal of productstream). Continuous fermentation minimizes the unproductive portions ofthe fermentation cycle, such as lag, growth, and turnaround time,thereby reducing capital cost, and reduces the number of inoculationevents, thus minimizing operational costs and risk associated with humanand process error.

Fermentation may be aerobic or anaerobic, depending on the requirementsof the bioproduct-producing microorganism.

In some embodiments, an immobilized butanol-producing Clostridium strainis fermented anaerobically in a continuous process as described herein.In one embodiment, the support is bone char. In another embodiment, thesupport is lava rock. In another embodiment, the support is aceramic/steel support material. In some embodiments, the Clostridiumstrain has an increased tolerance to butanol and/or an increased abilityto grow on the support, in comparison to a corresponding parent orwild-type strain, and/or in comparison to Clostridium saccharobutylicumB643, Clostridium saccharobutylicum P262, Clostridiumsaccharoperbutylacetonicum N1-4, Clostridium acetobutylicum 824, and/orClostridium beijerinckii 8524 when grown under identical conditions.

In some embodiments, reactor support materials and implementationthereof are designed so as to maximize reactor productivity. This mayinclude such features as maximizing fermentation gas removal efficiency,liquid-microorganism contact time, minimization of pressure drop, oroptimization for cleaning in place.

In some embodiments, bacterial strains, such as Clostridium strains, aresubstituted or rotated periodically to prevent or reduce the occurrenceof phage infections.

One or more bioreactors may be used in the bioproduct, e.g., biofuel,systems and processes described herein. When multiple bioreactors areused they can be arranged in series and/or in parallel. The advantagesof multiple bioreactors over one large bioreactor include lowerfabrication and installation costs, ease of scale-up production, greaterability to control the reaction, and greater production flexibility. Forexample individual bioreactors may be taken off-line for maintenance,cleaning, sterilization, and the like without appreciably impacting theoverall plant production schedule. In embodiments in which multiplebioreactors are used, the bioreactors may be run under the same ordifferent conditions.

In a parallel bioreactor arrangement, hydrolyzed feedstock is fed intomultiple bioreactors, and effluent from the bioreactors is removed. Theeffluent may be combined from multiple bioreactors for recovery of thebioproduct, e.g., biofuel, or the effluent from each bioreactor may becollected separately and used for recovery of the bioproduct.

In a series bioreactor arrangement, hydrolyzed feedstock is fed into thefirst bioreactor in the series, the effluent from the first bioreactoris fed into a second downstream bioreactor, and the effluent from eachbioreactor in the series is fed into the next subsequent bioreactor inthe series. The effluent from the final bioreactor in the series iscollected and may be used for recovery of the bioproduct, e.g., biofuel.The effluent may be treated between stages (e.g., primary to secondarybioreactor) to increase the overall productivity of the system.Nonlimiting examples of processes for such treatment include removal ofnon-condensable gases and pervaporation for the removal of solvents.

Each bioreactor in a multiple bioreactor arrangement can have the samespecies, strain, or mix of species or strains of microorganisms or adifferent species, strain, or mix of species or strains ofmicroorganisms compared to other bioreactors in the series. Thefermentation effluent is then removed and sent to separation andrecovery.

In some embodiments, feedstock is hydrolyzed in a multi-stage process asdescribed herein, and hydrolysate from each stage is fed to a separatebioreactor. The bioreactors to which the different hydrolysates are fedmay contain the same or different microbial species or strains. In oneembodiment, the bioreactors to which the different hydrolysates are fedcontain different microbial species or strains that have each beenoptimized for growth on the particular hydrolysate being fed to thatbioreactor. In some embodiments, different sets of multiple bioreactorsin series are fed hydrolysate from different stages of hydrolysis of thefeedstock.

In some embodiments, effluent can be recycled after the harvesting ofbioproduct, e.g., biofuel, and used to make the initial fermentationmedia or a feed stream for future fermentations, thereby allowingmaximum utilization of unassimilated and recovered nutrients andminerals. In some embodiments, product is isolated from the effluent andthe product reduced effluent is then used as a feedstock for the nextbioreactor in the series.

The order of bioreactors in a series can be adjusted to prevent orremove blockage due to excessive microbial growth. For example, when thefirst fermentor in a series reaches a high level of cell mass, it can beplaced second in the series to instead now receive effluent with highproduct concentration or reduced nutrient levels that may inhibitfurther cell growth. The timely shifting of the order of fermentors mayprevent cell overgrowth and blockage of the bioreactor, which mayincrease overall productivity of the system and/or reduce operationalcosts and burdens.

In a continuous process, it is possible to obtain a higher productivitythan in batch or fed-batch processes since the cell concentration andthe effluent flow rate can be varied independently of each other. In acontinuous fermentation, volumetric productivity is calculated bymultiplying the product concentration (herein, interchangeably calledthe “titer”) times the nutrient dilution rate (i.e., the rate ofchangeover of the volume of the bioreactor, or the inverse of thebioreactor residence time). The maximum achievable dilution rate isdetermined by the concentration of cell mass that one can stablymaintain in the bioreactor. At a constant dilution rate (i.e., nutrientconsumption rate), as one increases the fermentation titer that can bemaintained, the productivity is proportionately increased. However,there may be times when it is desirable to raise the dilution ratetemporarily, for a short time relative to the total duration of thefermentation, to remove gas, blockage, or “underperforming” cells.

Immobilized cell bioreactors allow higher concentrations of productivecell mass to accumulate and therefore, the bioreactors can be run athigh dilution rates, resulting in a significant improvement involumetric productivity relative to cultures of suspended cells. Since ahigh density, steady state culture can be maintained through continuousculturing, with the attendant removal of product containing fermentationbroth, smaller capacity bioreactors can be used. Bioreactors for thecontinuous fermentation of C. acetobutylicum are known in the art. (U.S.Pat. Nos. 4,424,275, and 4,568,643.)

Bioreactors for use in the bioproduct, e.g., biofuel, productionprocesses and systems herein are designed for continuous operation forat least about 100, 250, 300, 500, 750, 1,000, 1250, 1,500, 2,000,2,250, 2,500, 3,000, 4,000, 5,000 6,000, or 8,500 hours.

Bioreactor capacities contemplated for use in the bioproduct, e.g.,biofuel, production systems herein have a capacity (total nominalvolume) of about or at least about 100 L, 1000 L, 6,000 L, 10,000 L,46,000 L, 50,000 L, 100,000 L, 250,000 L, 270,000 L, 500,000 L, or1,000,000 L.

Numerous methods of fermentor inoculation are possible includingaddition of a liquid seed culture to the bottom or the top of thebioreactor and recirculation of the media to encourage growth throughoutthe bed. Other ways include the addition of a liquid seed culture orimpregnated solid support through a port located along the reactor'swall or integrated and loaded with the solid support material.Bioreactor effluent may also be used to inoculate an additionalbioreactor and in this case any residual fermentable materials may beconverted in the secondary reactor, increasing yield/recovery.

In a similar manner, support material may be added to the reactorthrough bottom, top, or side loading to replenish support material thatbecomes degraded or lost from the bioreactor.

Mixing of the bioreactor contents can be achieved through the spargingof sterile gas, e.g., carbon dioxide or N2, which may also serve toprevent contamination of the culture through the maintenance of positivepressure within the fermentor. The evolved gas (CO₂, H₂) from thefermentation may also be recovered and compressed for utilization in agas lift or other type reactor to maintain anaerobic, pressurized, wellmixed conditions.

Other techniques of mixing culture contents include the use of agitatorsor the recirculation of fermentation broth, particularly broth returnedto the bioreactor after the removal of a fermentation product. In someembodiments, the contents of the bioreactor are not mixed, but may relyon the production and movement of evolved gases to mix contents.

When fermentation conditions are vigorous, the gas produced may besufficient to prevent the ingress of oxygen to the reactor. For example,an unagitated reactor (e.g., 1000 L reactor), without temperaturecontrol and containing fermentation media and fermenting microorganisms,and that is open to the environment (e.g., a tote), may continue toconsume feed material and produce bioproducts (e.g., biofuel).

In some embodiments of the bioproduct, e.g., biofuel, productionprocesses and systems herein, immobilized microorganisms are cultured inpacked bed bioreactors, also known as plug-flow bioreactors. In otherembodiments, the microorganisms are cultured in expanded bedbioreactors. In other embodiments, the microorganisms are cultured influidized bed bioreactors. In still further embodiments, themicroorganisms are cultured in bioreactors that are designed to operatein “dual mode,” i.e., the bioreactors are capable of operating in eitherpacked bed or expanded/fluidized bed mode, e.g., during the same periodof operations to increase overall productivity (e.g., removal ofdetritus, removal of “underperforming” cells). Immobilized cellbioreactors use relatively small sized solid or semi-solid supports thatprovide a large surface area relative to the volume of the particles,allowing for the microorganisms immobilized on the particles to processlarge volumes of fluid.

In “packed bed” bioreactors, cells are immobilized on or in structuredpacking (e.g., Rashig rings, steel/ceramic wool) or semi-solid or solidparticles that because of particle size, mechanical restraint and/or lowfluid flow rates do not cause or allow for appreciable axial movement ofthe supporting material.

In contrast, fluidized and expanded bed reactors use semi-solid or solidsupport that is not substantially restrained mechanically so that withsufficient fluid flow, usually an upward-flowing stream, the particlesbecome suspended in the stream or “fluidized,” i.e., act as if they arepart of the fluid stream. The initial seed support particles may becomecovered by a biofilm over time and can become fully encapsulated by thebiofilm. In some cases, agglomeration of cellular mass may lead tosuspended biofilm particles in which there is no “seed” purposefullyintroduced. Fluid drag on the particles is the primary suspensionmechanism, but buoyancy forces can also contribute to the suspension ofthe particles. Typically, the bioreactors use vertical fluid motion tosuspend the particles, but other fluid motion is possible includingfluid flow at a direction perpendicular to the vertical axis of thebioreactor. The fluid velocity should be sufficient to suspend theparticles, but not large enough to carry them out of the vessel. Thefluidization of the bed allows the solid particles to move around thebioreactor, causing the fluid within the bioreactor to thoroughly mix.The magnitude of mixing depends on the extent of particle fluidizationachieved in the bioreactor. Fluidized and expanded bed bioreactorsrequire relatively larger amounts of energy to operate compared topacked beds because of the volume of fluid that must be circulated tokeep the particles suspended.

A “fluidized bed” bioreactor contains support particles with immobilizedmicroorganisms fluidized throughout the full volume of the bioreactor.Particles exit the bioreactor through the outflow and have to beseparated from the effluent liquid and returned to the bioreactor.Support material can be removed, optionally cleaned, and recovered fromthe effluent stream through the use of settling tanks, dissolved airflotation (DAF) systems, centrifuges, hydrocyclones, filters (e.g.,rotary drum), filter aids, dryers, or distillation apparatus.

An “expanded bed” bioreactor contains support particles with immobilizedmicroorganisms fluidized in the bioreactor, but the bioreactor isdesigned such that the particles are retained in the bioreactor and donot exit through the outflow. An expanded bed bioreactor contains aparticle disengagement zone for separating the fluidized particles fromthe fluid, thereby retaining the particles within the bioreactor. Insome embodiments, separation of the particles from the fluid includesslowing the velocity of the fluid. In some embodiments, this isaccomplished by increasing the cross sectional area of the bioreactor.As the fluid velocity slows, the particles start to settle out of thefluid. The top section of the particle disengagement zone is free ofparticles. An outlet can be located at this top portion to removeeffluent. In some embodiments, particles are retained by includingfilters or screens within the bioreactor.

A dual mode, packed bed-fluidized or expanded bed bioreactor allows forthe option of conducting fermentations in either mode for the course ofa whole fermentation run. Alternately, the fermentation can alternatebetween modes during the course of a single fermentation. Dual modebioreactors can have reduced energy usage compared to conventionalfluidized or expanded bed bioreactors because fluidization with itsrequisite increased energy requirement need only be performed, forexample, at relatively high cell densities, high product concentrations,or when pH or nutrient inhomogeneities develop that can be correctedthrough increased mixing of the bioreactor contents.

In various embodiments, a bioreactor may be configured in a vertical,horizontal, or inclined configuration, to maximize gas/liquid separationand/or to improve elution of evolved fermentation gas to improve overalloperation and metrics for the production process, e.g., titer,productivity, and/or yield of bioproduct, e.g., biofuel, production. Inone embodiment, a bioreactor may be configured as a “trickle bedreactor,” in which the material to be reacted is fed into the bed by aslow flow.

In some embodiments, the amount of a bioproduct such as a biofuel, e.g.,biobutanol, produced per amount of sugar fed to a bioreactor may beabout or at least about 0.1, 0.15, 0.2 0.25, 0.3, 0.33, 0.35, 0.4, 0.45,or 0.5 grams per gram sugar converted, subject to the particularreaction stoichiometry. In some embodiments, the fermentation mayutilize about or at least about 40, 50, 60, 65, 70, 75, 80, 85, 90, 95,96, 97, 98, or 99% of the available sugar. In some embodiments, about orat least about 20, 30, 40, 50, 60, 70, 80, 90, or 95 gallons of biofuel,e.g., biobutanol, is produced per tonne of feedstock, or an amount thatapproaches the theoretical limit, depending on the feedstock that isused.

In some embodiments, a bioproduct such as a biofuel, e.g., biobutanol,is produced at a productivity of about or at least about 1, 2, 3, 5, 6,7, 8, 9, 10, 12, 15, 20, 25, 30, 35, 40, 45, or 50 g/L/h.

In some embodiments, bioreactor volumetric productivity and bioproduct,e.g., biofuel, for example, butanol, titer may be improved by reducingthe particle size of the immobilized support, which can increaseavailable surface area for cell growth, resulting in higher bioreactorproductivity. By fluidizing the solid support in fluidized or expandedbed mode, and by using smaller particles with greater size uniformity,mixing can be greatly improved, permitting optimization of nutrients andpH, further improving fermentation performance.

Some Clostridium strains convert sugars into butanol, acetone, andethanol in a 6:3:1 mass ratio. In some embodiments, strains used in thesystems and processes described herein produce a larger proportion ofbutanol relative to acetone—for example, approximately 75%-25%—with verylittle ethanol (about 2%). In other embodiments, the ratio of butanol toacetone to ethanol can be about or at least about 58:12:1. In someembodiments, the ratio of butanol to acetone to ethanol is greater thanabout 58:12:1. In some embodiments, the distribution of productsproduced by the Clostridium strain can be such that the amount ofbutanol is at least about 70%, the amount of acetone is at least about25%, and the amount of ethanol is less than about 5%. This higherbutanol selectivity results in a higher yield of butanol per unit weightof feedstock. Furthermore, selecting strains having a higher butanoltolerance and higher butanol selectivity in an immobilized environmentcan result in a higher concentration of butanol in the fermentationbroth leaving the reactor, thereby requiring less energy in the productseparation phase, and reducing operating costs, cooling water use, andlifecycle GHG emissions.

Fermentation Media

Fermentation media for the production of bioproduct, e.g., biofuel,products contain feedstock, e.g., a hydrolyzed feedstock, as describedherein, as a source of fermentable carbohydrate molecules.

As known in the art, in addition to an appropriate carbon source,fermentation media must contain suitable nitrogen source(s), mineralsalts, cofactors, buffers, and other components suitable for the growthof the cultures and promotion of the enzymatic pathway necessary for theproduction of the desired target (e.g., biofuel, such as butanol). Insome embodiments, salts and/or vitamin B12 or precursors thereof areincluded in the fermentation media. In some cases, hydrolyzed feedstockmay contain some or all of the nutrients required for growth, minimizingor obviating the need for additional supplemental material.

The nitrogen source may be any suitable nitrogen source, including butnot limited to, ammonium salts, yeast extract, corn steep liquor (CSL),and other protein sources including, but not limited to, denaturedproteins recovered from distillation of fermentation broth or extractsderived from the residual separated microbial cell mass recovered afterfermentation (Clostridium extract). Phosphorus may be present in themedium in the form of phosphate salts, such as sodium, potassium, orammonium phosphates. Sulfur may be present in the medium in the form ofsulfate salts, such as sodium or ammonium sulfates. Additional saltsinclude, but are not limited to, magnesium sulfate, manganese sulfate,iron sulfate, magnesium chloride, calcium chloride, manganese chloride,ferric chloride, ferrous chloride, zinc chloride, cupric chloride,cobalt chloride, and sodium molybdate. The growth medium may alsocontain vitamins such as thiamine hydrochloride, biotin, andpara-aminobenzoic acid (PABA). The growth medium may also contain one ormore buffering agent(s) (e.g., MES), one or more reducing agent(s)(e.g., cysteine HCl), and/or sodium lactate, which may serve as a carbonsource and pH buffer.

Culture Conditions

Optimal culture conditions for various industrially importantmicroorganisms are known in the art. As required, the culture conditionsmay be anaerobic, microaerotolerant, or aerobic. Aerobic conditions arethose that contain oxygen dissolved in the media such that an aerobicculture would not be able to discern a difference in oxygen transferwith the additional dissolved oxygen, and microaerotolerant conditionsare those where some dissolved oxygen is present at a level below thatfound in air or air saturated solutions and frequently below thedetection limit of standard dissolved oxygen probes, e.g., less than 1ppm. The cultures can be agitated or left undisturbed. Typically, the pHof the media changes over time as the microorganisms grow in number,consume feedstock and excrete organic acids. The solubility of CO₂,produced during fermentation or present in the media, can also affectpH. The pH of the media can be modulated by the addition of bufferingcompounds to the initial fermentation media in the bioreactor or by theactive addition of acid or base to the growing culture to keep the pH ina desired range. Growth of the culture may be monitored by measuring theoptical density, typically at a wavelength of 600 nm, or by othermethods known in the art.

For converting sugars to ethanol using S. cerevisiae, generally, thetemperature is about 25° C. to about 35° C. Useful pH ranges for theconversion medium include about 4.0 to about 6.0, about 4.5 to about6.0, and about 5.5 to about 5.8. The culture is grown under anaerobicconditions without agitation.

Clostridium fermentations are generally conducted under anaerobicconditions. For example, ABE fermentations by C. acetobutylicum aretypically conducted under anaerobic conditions at a temperature in therange of about 25° C. to about 40° C. Historically, suspension culturesdid not use agitators, but relied on evolved or sparged gas to mix thecontents of the bioreactors. Cultures, however, can be agitated toensure more uniform mixing of the contents of the bioreactor. Forimmobilized cultures, a bioreactor may be run without agitation in afixed bed (plug flow) or fluidized/expanded bed (well-mixed) mode.Thermophilic bacterial fermentations can reach temperatures in the rangeof about 50° C. to about 80° C. In some embodiments, the temperaturerange is about 55° to about 70° C. In some embodiments, the temperaturerange is about 60° C. to about 65° C. For example, Clostridium speciessuch as C. thermocellum or C. thermohydrosulfuricum may be grown atabout 60° C. to about 65° C. The pH of the Clostridium growth medium canbe modulated by the addition of buffering compounds to the initialfermentation media in the bioreactor or by the active addition of acidor base to the growing culture to keep the pH in a desired range. Forexample, a pH in the range of about 3.5 to about 7.5, or about 5 toabout 7, may be maintained in the medium for growth of Clostridium.

Immobilization of Microorganism on Solid Support

Immobilization of the microorganism, from spores or vegetative cells,can be by any known method. In one embodiment, entrapment or inclusionin the support is achieved by polymerizing or solidifying a spore orvegetative cell containing solution. Useful polymerizable orsolidifiable solutions include, but are not limited to, alginate,K-carrageenan, chitosan, polyacrylamide, polyacrylamide-hydrazide,agarose, polypropylene, polyethylene glycol, dimethyl acrylate,polystyrene divinyl benzene, polyvinyl benzene, polyvinyl alcohol, epoxycarrier, cellulose, cellulose acetate, photocrosslinkable resin,prepolymers, urethane, and gelatin.

In another embodiment, the microorganisms are incubated in growth mediumwith a support. Useful supports include, but are not limited to, bonechar, cork, clay, resin, sand, porous alumina beads, porous brick,porous silica, celite (diatomaceous earth), polypropylene, polyesterfiber, ceramic, (e.g., porous ceramic, such as porous silica/aluminacomposite), lava rock, vermiculite, ion exchange resin, coke, naturalporous stone, macroporous sintered glass, steel, zeolite, engineeredthermal plastic, concrete, glass beads, Teflon, polyetheretherketone,polyethylene, wood chips, sawdust, cellulose fiber (pulp), or othernatural, engineered, or manufactured products. The microorganisms mayadhere to the support and form an aggregate, e.g., a biofilm.

In another embodiment, the microorganism is covalently coupled to asupport using chemical agents like glutaraldehyde, o-dianisidine (U.S.Pat. No. 3,983,000), polymeric isocyanates (U.S. Pat. No. 4,071,409),silanes (U.S. Pat. Nos. 3,519,538 and 3,652,761), hydroxyethyl acrylate,transition metal-activated supports, cyanuric chloride, sodiumperiodate, toluene, or the like. See also U.S. Pat. Nos. 3,930,951 and3,933,589.

In one embodiment, immobilized spores, such as those of Clostridium,e.g., C. acetobutylicum, are activated by thermal shock and thenincubated under appropriate conditions in a growth medium wherebyvegetative growth ensues. These cells remain enclosed in or on the solidsupport. After the microorganisms reach a suitable density andphysiological state, culture conditions can be changed for bioproduct,e.g., biofuel, production. If the immobilized cells lose bioproduct,e.g., biofuel, production, they can be reactivated by first allowing thecells to sporulate before repeating the thermal shock and culturesequence.

Vegetative cells can be immobilized in different phases of their growth.For microorganisms that display a biphasic culture, such as C.acetobutylicum with its acidogenic and solventogenic phases, cells canbe immobilized after they enter the desired culture phase in order tomaximize production of the desired products, where in the case of C.acetobutylicum it is the organic acids acetic acid and butyric acid inthe acidogenic phase and the solvents acetone, butanol and ethanol inthe solventogenic phase. Alternatively, biphasic cells can beimmobilized in the acidogenic phase and then adapted for solventproduction.

In some embodiments, microorganisms to be immobilized in a bioreactorare introduced by way of a cell suspension. Generally, thesemicroorganisms are dispersed in the media as single cells or smallaggregates of cells. In other embodiments, the microorganisms areintroduced into the bioreactor through the use of suspended particlesthat are colonized by the microorganisms. These suspended particles canbe absorbed onto the solid support and frequently are of sufficientlysmall size that they can enter and become immobilized in the porestructures of the solid support. Typically, regardless of the suspendedparticle size, microorganisms can be transferred by contact with thesolid support. A biofilm on the introduced particles can transfer to andcolonize these new surfaces. In some embodiments, the desiredcharacteristics of the microorganisms can only be maintained byculturing on a solid support, thereby necessitating the use of smallcolonized particle suspensions for seeding a solid support in abioreactor.

Support for Immobilized Microbial Growth

In some embodiments, a bioproduct, e.g., biofuel, producingmicroorganism is grown in an immobilized form on a solid or semi-solidsupport material in a bioreactor as described herein. In someembodiments, the support comprises a porous material. Non-limitingexamples of suitable support materials include bone char, syntheticpolymers, natural polymers, inorganic materials, and organic materials.

Natural polymers include organic materials such as cellulose,lignocellulose, hemicellulose, and starch. Organic materials includefeedstock such as plant residue and paper. Composites of two or morematerials may also be used such as mixtures of synthetic polymer withnatural plant polymer.

Examples of semi-solid media include alginate, ic-carrageenan andchitosan, polyacrylamide, polyacrylamide-hydrazide, agarose,polypropylene, polyethylene glycol, dimethyl acrylate, polystyrenedivinyl benzene, polyvinyl benzene, polyvinyl alcohol, epoxy carrier,cellulose, cellulose acetate, photocrosslinkable resin, prepolymers,urethane, and gelatin. Examples of solid support include cork, clay,resin, sand, porous alumina beads, porous brick, porous silica, celite,wood chips or activated charcoal.

Suitable inorganic solid support materials include inorganic materialswith available surface hydroxy or oxide groups. Such materials can beclassified in terms of chemical composition as siliceous or nonsiliceousmetal oxides. Siliceous supports include, inter alia, glass, colloidalsilica, wollastonite, cordierite, dried silica gel, bentonite, and thelike. Representative nonsiliceous metal oxides include alumina, hydroxyapatite, and nickel oxide.

In some embodiments, the support material is selected from bone char,polypropylene, steel, diataomaceous earth, zeolite, ceramic, (e.g.,porous ceramic, such as porous silica/alumina composite), engineeredthermal plastic, clay brick, concrete, lava rock, wood chips, polyesterfiber, glass beads, Teflon, polyetheretherketone, polyethylene,vermiculite, ion exchange resin, cork, resin, sand, porous aluminabeads, coke, natural porous stone, macroporous sintered glass, or acombination thereof. In one embodiment, the support material is bonechar. Useful support material has a high surface area to volume ratiosuch that a large amount of active, productive cells can accumulate inthe bioreactor. Useful supports may contain one or more macrostructuredcomponents containing one or more useful support material(s) thatpromotes good fluid-mechanical properties, for example, a wiremesh/gauze packing material used for traditional distillation towerpacking.

In some embodiments, the support material comprises a surface area of atleast about 100 m²/m³. In some embodiments, the support materialcomprises a bulk density of at least about 0.15 g/cm³. In someembodiments, the support material comprises a ball-pan hardness numberof at least about 60. In some embodiments, the support materialcomprises a yield strength of at least about 20 MPa.

The particle size for the support material will vary depending uponbioreactor configuration and operation parameters. In some embodiments,the support material is sized by sieving. In some embodiments, theparticles are classified by the sieve number of the mesh that they canpass through. In some embodiments, the particles are sieved with a meshthat has a U.S. Sieve Number of 3½, 4, 5, 6, 7, 8, 10, 12, 14, 16, 18,20, 25, 30, 35, 40, 45, 50, 60, or 70. In some embodiments, theparticles are sieved at least twice, first using a mesh with largeropenings followed by a mesh with smaller openings to yield particleswithin a defined particle size distribution range. In some embodiments,the particles are at least about 100 μm, 200 μm, 300 μm, 400 μm, 500 μm,600 μm, 700 μm, 800 μm, 900 μm, 1000 μm, 1,100 μm, 1,200 μm, 1,300 μm,1,400 μm, 1,500 μm, 1,600 μm, 1,700 μm, 1,800 μm, 1,900 μm, 2,000 μm,3,000 μm, 4,000 μm, 5,000 μm, 6,000 μm, 7,000 μm, 8000 μm, 9,000 μm,10,000 μm, 12,500 μm, 15,000 μm, 17,500 μm, 20,000 μm, 22,500 μm, or25,000 μm in diameter. In some embodiments, the particles are less thanabout 100 μm, 200 μm, 300 μm, 400 μm, 500 μm, 600 μm, 700 μm, 800 μm,900 μm, 1000 μm, 1,100 μm, 1,200 μm, 1,300 μm, 1,400 μm, 1,500 μm, 1,600μm, 1,700 μm, 1,800 μm, 1,900 μm, 2,000 μm in diameter. In furtherembodiments, at least about 80%, 85%, 90%, 95%, or 100% of the particlehave diameters that are in the range of about 100-400 μm, 100-600 μm,100-800 μm, 200-500 μm, 200-800 μm, 200-1000 μm, 400-800 μm, 400-1000μm, 500-1000 μm, 600-1,200 μm, 800-1,400 μm, 1,000-1,500 μm, 1,000-2000μm, 2,000-4,000 μm, 4,000-6,000 μm, 5,000-12,000 μm, 3,000-15,000 μm, or6,000-25,000 μm. In some embodiments, the particle diameters are theequivalent diameters, a parameter that takes into account the irregularshapes of the individual particles.

Ideally, the semi-solid or solid support material should have a highsurface area. This can be achieved through the use of small sizedparticles, particles with high porosity, or a combination thereof. Insome embodiments, the surface area of the particles is at least about0.003 m²/g, 0.01 m²/g, 0.02 m²/g, 0.05 m²/g, 0.1 m²/g, 0.5 m²/g, 1 m²/g,5 m²/g, 10 m²/g, 25 m²/g, 50 m²/g, 75 m²/g, 100 m²/g, 125 m²/g, 150m²/g, 175 m²/g, 200 m²/g, 225 m²/g, 250 m²/g, 275 m²/g, 300 m²/g, 325m²/g, 350 m²/g, 375 m²/g, 400 m²/g, 425 m²/g, 450 m²/g, 500 m²/g, 600m²/g, 700 m²/g, 800 m²/g, 900 m²/g, 1000 m²/g, or 2000 m²/g.Additionally, the bulk density should be sufficiently high so that thesmallest particles settle out of the fluid stream in the columnexpansion zone and/or particle disengagement zone and are therebyretained in the bioreactor. In some embodiments, the bulk density of thesupport is at least about 0.1 g/cm³, 0.2 g/cm³, 0.3 g/cm³, 0.4 g/cm³,0.5 g/cm³, 0.6 g/cm³, 0.7 g/cm³, 0.8 g/cm³, 0.9 g/cm³, 1.0 g/cm³, 1.1g/cm³, 1.2 g/cm³, or 1.3 g/cm³. The support material should havesufficient hardness to resist abrasion and thereby avoid appreciabledust formation when the support particles touch or collide with eachother. In some embodiments, the support has a ball-pan hardness numberof at least about 20, 40, 60, 80, 100, 120, 140, 160 or 200. The supportmaterial should also have sufficient tensile strength to resistshattering due to internal stresses, which may be caused by the growthof biofilms inside support material pores. In some embodiments, thesupport has a yield strength of at least about 20 MPa, 40 MPa, 60 MPa,80 MPa, 100 MPa, 120 MPa, 140 MPa, 160 MPa, 180 MPa, 200 MPa, 300 MPa,or 400 MPa. The support material should also have the ability to resistbeing crushed by the accumulated weight of material above it. Crushstrength is another measurement of the mechanical strength of thesupport and is typically a function of the composition, shape, size, andporosity of the material (increase in port volume may negatively impactparticle strength). In some embodiments, the crush strength is at leastabout 8 kg.

In some embodiments, the support material is chosen to support growth ofthe fermenting bioproduct, e.g., biofuel, producing microorganism as abiofilm. The biofilm may grow on exterior surfaces of support particles,in the fluid space between support particles, and/or on surfaces in theinterior of pores of the support material.

Microorganisms

The systems and processes described herein include one or moremicroorganism(s) that is (are) capable of producing a bioproduct, e.g.,biofuel. In embodiments in which two or more microorganisms are used,the microorganisms may be the same or different microbial species and/ordifferent strains of the same species.

In some embodiments, the microorganisms comprise bacteria or fungi. Insome embodiments, the microorganisms comprise a single species. In someembodiments, the microorganisms comprise a mixed culture of strains fromthe same species. In some embodiments, the microorganism comprises amixed culture of different species. In some embodiments, themicroorganism comprises an environmental isolate or strain derivedtherefrom.

In some embodiments of the processes and systems described herein,different species or strains, or different combinations of two or morespecies or strains, are used in different bioreactors with differenthydrolyzed feedstocks as a carbohydrate source.

In some embodiments, a fungal microorganism is used, such as a yeast.Examples of yeasts include, but are not limited to, Saccharomycescerevisiae, S. bayanus, S. carlsbergensis, S. Monacensis, S.Pastorianus, S. uvarum and Kluyveromyces species. Other examples ofanaerobic or aerotolerant fungi include, but are not limited to, thegenera Neocallimastix, Caecomyces, Piromyces and other rumen derivedanaerobic fungi.

In some embodiments, a bacterial microorganism is used, includingGram-negative and Gram-positive bacteria. Non-limiting examples ofGram-positive bacteria include bacteria found in the genera ofStaphylococcus, Streptococcus, Bacillus, Mycobacterium, Enterococcus,Lactobacillus, Leuconostoc, Pediococcus, and Propionibacterium.Non-limiting examples of specific species include Enterococcus faeciumand Enterococcus gallinarium. Non-limiting examples of Gram-negativebacteria include bacteria found in the genera Pseudomonas, Zymomonas,Spirochaeta, Methylosinus, Pantoea, Acetobacter, Gluconobacter,Escherichia and Erwinia.

In one embodiment, the bacteria are Clostridium species, including butnot limited to, Clostridium saccharobutylicum, Clostridiumacetobutylicum, Clostridium beijerinckii, Clostridium puniceum, andenvironmental isolates of Clostridium.

Further examples of species of Clostridium contemplated for use in thisinvention can be selected from C. aurantibutyricum, C. butyricum, C.cellulolyticum, C. phytofermentans, C. saccharolyticum, C.saccharoperbutylacetonicum, C. tetanomorphum, C. thermobutyricum, C.thermocellum, C. puniceum, C. thermosaccharolyticum, and C. pasterianum.

Other bacteria contemplated for use in the processes and systems hereininclude Corynebacteria, such as C. diphtheriae, Pneumococci, such asDiplococcus pneumoniae, Streptococci, such as S. pyogenes and S.salivarus, Staphylococci, such as S. aureus and S. albus, Myoviridae,Siphoviridae, Aerobic Spore-forming Bacilli, Bacilli, such as B.anthracis, B. subtilis, B. megaterium, B. cereus, Butyrivibriofibrisolvens, Anaerobic Spore-forming Bacilli, Mycobacteria, such as M.tuberculosis hominis, M. bovis, M. avium, M. paratuberculosis,Actinomycetes (fungus-like bacteria), such as, A. israelii, A. bovis, A.naeslundii, Nocardia asteroides, Nocardia brasiliensis, the Spirochetes,Treponema pallidium, Treponema pertenue, Treponema carateum, Borreliarecurrentis, Leptospira icterohemorrhagiae, Leptospira canicola,Spirillum minus, Streptobacillus moniliformis, Trypanosomas,Mycoplasmas, Mycoplasma pneumoniae, Listeria monocytogenes,Erysipelothrix rhusiopathiae, Streptobacillus monilformis, Donvaniagranulomatis, Bartonella bacilliformis, Rickettsiae, Rickettsiaprowazekii, Rickettsia mooseri, Rickettsia rickettsiae, and Rickettsiaconori. Other suitable bacteria may include Escherichia coli, Zymomonasmobilis, Erwinia chrysanthemi, and Klebsiella planticola.

In some embodiments, the microorganisms comprise the genera Clostridium,Enterococcus, Klebsiella, Lactobacillus, or Bacillus. In someembodiments, the microorganisms comprise Clostridium acetobutylicum,Clostridium beijerinckii, Clostridium puniceum, Clostridiumsaccharobutylicum, Enterococcus faecium, Enterococcus gallinarium,Clostridium aurantibutyricum, Clostridium aurantibutyricum, Clostridiumtetanomorphum, or Clostridium thermosaccharolyticum.

In some embodiments, the microorganisms are obligate anaerobes.Non-limiting examples of obligate anaerobes include Butyrivibriofibrosolvens and Clostridium species.

In other embodiments, the microorganisms are microaerotolerant and arecapable of surviving in the presence of small concentrations of oxygen.In some embodiments, microaerobic conditions include, but are notlimited, to fermentation conditions produced by sparging a liquid mediawith a gas of at least about 0.01% to at least 5% or more O₂ (e.g.,0.01%, 0.05%, 0.10%, 0.50%, 0.60%, 0.70%, 0.80%, 1.00%, 1.20%, 1.50%,1.75%, 2.0%, 3%, 4%, 5% or more O₂). In another aspect, the microaerobicconditions include, but are not limited to, culture conditions with atleast about 0.05 ppm dissolved O₂ or more (e.g., 0.05, 0.075, 0.1, 0.15,0.2, 0.3, 0.4, 0.5, 0.6, 0.8, 1.0, 2.0, 3.0, 4.0, 5.0, 8.0, 10.0, ppm ormore).

Microbial strains may be optimized, mutated, or otherwise selected fordesirable characteristics. For example, parent strains of bacteria andfungi may be used for the development of higher product tolerantmutants. See, for example, PCT/US09/40050. Sources of such parentstrains include established culture collections, and researchers inuniversities, government institutions, or companies.

Alternatively, parent strains can be isolated from environmental samplessuch as wastewater sludge from wastewater treatment facilities includingmunicipal facilities and those at chemical or petrochemical plants. Thelatter are especially attractive as the isolated microorganisms can beexpected to have evolved over the course of numerous generations in thepresence of high product concentrations and thereby have alreadyattained a level of desired product tolerance that may be furtherimproved upon.

Parent strains may also be isolated from locations of naturaldegradation of naturally occurring feedstocks and compounds (e.g., awoodpile, a saw yard, under fallen trees, landfills). Such isolates maybe advantageous since the isolated microorganisms may have evolved overtime in the presence of the feedstock and thereby have already attainedsome level of conversion and tolerance to these materials that may befurther improved upon.

Individual species or mixed populations of species can be isolated fromenvironmental samples.

In some embodiments, environmental isolates and/or microbial consortiumsare used to generate microbial consortiums that have increased producttolerance. Isolates, including microbial consortiums can be collectedfrom numerous environmental niches including soil, rivers, lakes,sediments, estuaries, marshes, industrial facilities, etc. In someembodiments, the microbial consortiums are strict anaerobes. In otherembodiments, the microbial consortiums are obligate anaerobes. In someembodiments, the microbial consortiums are facultative anaerobes. Instill other embodiments, the microbial consortiums do not containspecies of Enterococcus or Lactobacillus.

When mixed populations of specific species or genera are used, aselective growth inhibitor for undesired species or genera can be usedto prevent or suppress the growth of these undesired microorganisms.

In some embodiments, cocultures are utilized. For example, onemicroorganism may secrete enzymes into the media that break down afeedstock into constituent compounds that can be utilized by anothermicroorganism. For example, ethanol may be produced from a coculture ofClostridium thermocellum and C. thermohydrosulfuricum (Eng et al. (1981)Applied and Environmental Microbiology 41 (6): 1337-1343).

In some embodiments, the microorganisms comprise one or moreheterologous genes, the expression of which increases the producttolerance of the microorganisms. In some embodiments, the one or moreheterologous genes are introduced into the microorganism beforeadaptation on a solid support or selection for product tolerance, whilein other embodiments, the one or more heterologous genes are introducedinto the microorganisms after adaptation or selection for producttolerance.

In some embodiments, the microorganisms are engineered to over-expressendogenous genes that increase the product tolerance of themicroorganisms. In some embodiments, the microorganisms compriseadditional copy numbers of endogenous genes that increase resistance toproducts. In certain embodiments, the product tolerant microorganismsare not E. coli and the heterologous or over-expressed genes are notyfdE, yhhL, yhhM, and csrC. In other embodiments, the microorganisms arenot recombinant microorganisms that have increased expression of heatshock proteins. In still other embodiments, the microorganisms are notrecombinant microorganisms that comprise a heterologous gene thatencodes a polypeptide that exports butanol out of the microorganism.

In some embodiments, the microorganism is a Clostridium strain thatpossesses one or more phenotypic characteristics selected from increasedbutanol tolerance, increased tolerance to inhibitors of fermentation,low butyric acid and/or acetic acid accumulation, increased stability incontinuous fermentation, increased butanol titer, production of biofuelwith increased butanol to acetone ratio, increased yield of butanol perunit of feedstock, increased yield of butanol per unit of cellularbiomass, increased oxygen tolerance, increased ability to adhere to asolid support, and decreased ability to sporulate, relative to awild-type or parent Clostridium strain and/or relative to Clostridiumsaccharobutylicum B643 (Contag et al. (1990) Applied EnvironmentalMicrobiology 56:3760-65), Clostridium saccharobutylicum P262 (ATCCBAA-11), Clostridium saccharoperbutylacetonicum N1-4 ATCC 27021,Clostridium acetobutylicum ATCC 824 and/or Clostridium beijerinckii ATCC51743.

In some embodiments, the microorganism is a strain, for example, aClostridium strain, e.g., Clostridium acetobutylicum, Clostridiumsaccharobutylicum, Clostridium saccharoperbutylacetonicum, orClostridium beijerinckii, having tolerance to at least about 2%, 2.5%,5%, 10%, 12%, or 15% biofuel, in the growth medium by weight, forexample, tolerance to at least about 2%, 2.5%, 5%, 10%, 12%, or 15%butanol in the growth medium by weight.

In some embodiments, the microorganism is a mutant strain having atleast about 125%, 150%, 200%, 250%, 500%, or 1,000% increased toleranceto a biofuel in the growth medium, for example, at least about 125%,150%, 200%, 250%, 500%, or 1,000% increased tolerance to butanol in thegrowth medium, measured by growth of the microorganism in comparison toa corresponding non-mutant microorganism, for example, the correspondingparent or wild-type microorganism, when grown under identicalconditions. In some embodiments, the mutant strain is a Clostridiumstrain, e.g., Clostridium acetobutylicum, Clostridium saccharobutylicum,Clostridium saccharoperbutylacetonicum, or Clostridium beijerinckii,having at least about 125%, 150%, 200%, 250%, 500%, or 1,000% increasedtolerance to a biofuel, e.g., butanol, in the growth medium, incomparison to Clostridium saccharobutylicum B643, Clostridiumsaccharobutylicum P262, Clostridium saccharoperbutylacetonicum N1-4 ATCC27021, Clostridium acetobutylicum ATCC 824, and/or Clostridiumbeijerinckii ATCC 51743, when grown under identical conditions.

In some embodiments, a strain that produces a bioproduct, e.g., abiofuel, such as butanol, efficiently from pentoses, such as xylose andother sugars found in hemicellulose hydrolysates, may be obtained byenvironmental isolation or mutation of a parent strain. Some strains maymetabolize insoluble substrates, e.g., xylan, utilizing endogenousenzymatic activities, such as xylanase and/or amylase. Other strains maydegrade inulin and/or pectin without addition of exogenous enzymes.Other strains may metabolize a variety of sugars and convert them toproducts. Such strains may be used as a basis for strain engineering ormutagenesis. A diverse strain library can allow for the rotation ofstrains in fermentation, preventing phage contamination and providingdiversity for metabolism of different feed hydrolysates.

Recovery Processes

The fermentation effluent containing the bioproduct may be concentratedand/or purified. In some embodiments, the product is concentrated priorto further purification using any suitable concentration technique knownin the art, including but not limited to distillation, steam strippingdistillation, mechanical vapor recompression (MVR) distillation, vacuumdistillation, pervaporation, and liquid-liquid extraction.

In one embodiment, the bioproduct is a biofuel, for example, butanol,ethanol, and/or acetone. In some embodiments, primary components of thefermentation effluent are butanol, acetone, ethanol, butyric acid, andacetic acid, all of which may be recovered and used as startingmaterials for downstream chemical syntheses to produce derivativesand/or further chemical products. Secondary components of thefermentation effluent include, but are not limited to, proteins andother products of metabolic pathways, which may also be used as startingmaterials for production of derivatives or further chemical products.Secondary components include, but are not limited to, solvents,biomolecules (e.g., proteins (e.g., enzymes), polysaccharides), organicacids (e.g., formate, acetate, butyrate, propionate, succinate),alcohols (e.g., methanol, propanol, isopropanol, hexanol), vitamins,sugar alcohols (e.g., xylitol). Further, chemical compounds generatedduring acid hydrolysis of feedstock, including but not limited to,furfural, formic acid, levulinic acid, and HMF, may also be separatedfrom the fermentation effluent and used as starting materials forproduction of derivatives or further chemical products.

In some embodiments, fermentation product streams from multiplebioreactors or series of bioreactors are combined prior to furtherpurification. In some embodiments, fermentation product streams frommultiple bioreactors or series of bioreactors are fed to separatepurification units. For example, a fermentation product stream from afirst bioreactor processing C5 sugars can be combined with fermentationproducts from a second bioreactor processing C5 and C6 sugars.Alternatively, the product streams from the first and second bioreactorsmay be processed separately.

In other configurations, fermentation broth may be separated fromproducts in situ (i.e., extractive fermentation) by any of a variety ofmethods (e.g., LLE (liquid-liquid extraction), vacuum distillation,stripping, pervaporation), to increase the total productivity of theoverall conversion process. For example, butanol and other products maybe recovered from the bioreactor by condensation of the sparging andnaturally occurring gases.

In other configurations, one or more processing steps may be carried outbetween fermentation stages (e.g., between primary and secondaryreactors in a series) to enhance the overall system from an economic,operability, maintenance, energy, and/or water use perspective.

In some embodiments, MVR distillation is used for concentration of abioproduct, such as a biofuel, from the microbial fermentation medium.In this approach, overhead vapors generated as part of the distillationprocess are mechanically compressed, and the resulting latent heatreleased from the condensation process is supplied to the evaporationprocess. In some embodiments, MVR reduces separation energy requirementsby at least about 80% in comparison to conventional distillation.

In some embodiments, a conventional distillation process is used for theremaining product separation, optionally with thermally cascaded heatintegration. Previously, separation of biobutanol from fermentationmedia has been hindered due to the impact of secondary compounds on theseparation process. Distillation avoids this issue since surfacechemistry is not the basis for the separation.

In some embodiments, process equipment is selected to optimize energy,water, and/or other metric of interest. In the case of energy use, thismay include the addition of heat exchangers to recover stream enthalpyfor useful purposes, or to avoid complete condensation or evaporation offeed and/or overhead streams.

In one embodiment of a butanol recovery process, fermentation broth(effluent) is passed from a fermentation module to a product recoverymodule in which solvents (e.g., butanol, acetone, ethanol) and othervolatile compounds are separated from water and less volatile compoundssuch as biomass residue, carbohydrates and hydrolysis generated sugars.Some water accompanies the solvents and other volatiles in the overheadof the product recovery module. The volatile-water stream may or may notbe passed to a decanting operation to increase the effectiveness andefficiency of the remaining product separation. The product recoveryoverhead stream is passed to a high-low volatile splitter module inwhich two (or more) streams are generated—a light fraction, a heavyfraction and potentially a mixed solvent side draw. The mixed solventside draw may contain primarily acetone, ethanol, and water. The lightfraction contains primarily acetone, ethanol and water. Optionally, thelight fractions are sent to an acetone column in which acetone isseparated from the other components in the feed stream (e.g., ethanoland water). The lower volatility stream exiting the high-low volatilitysplitter (heavy fraction) is passed to a decanter where a phaseseparation occurs. The upper phase is an organic rich phase which ispassed to a butanol column. For example, the upper phase may containabout 80% butanol and about 20% water. The operating temperature andpressure affect the partitioning of compounds in the phases. The phaseseparation unit may be in fluid contact with a butanol column and awater column. The butanol column separates butanol from an overheadstream primarily comprised of a butanol-water azeotropic stream. Theazeotrope stream is returned to the decanter (phase separationoperation) for further separation. The aqueous phase of the decanter,which may contain nearly or about 9% butanol and about 89% water, ispassed to the aqueous column in which water is separated from a mostlybutanol-water azeotrope. The butanol-water azeotrope is returned to thedecanter for further processing.

In some embodiments, butyric acid is removed from the butanol productstream formed in the distillation process. In one embodiment, butyricacid is adsorbed from the butanol product stream. For example, atertiary amine ion-exchange resin may be used for adsorption of butyricacid. In another embodiment, butanol and butyric acid are separated bydistillation. In a further embodiment, butanol and butyric acid areseparated by pervaporation. In one embodiment, the butyric acid isremoved and may be sold as a chemical product. In another embodiment,the butyric acid is returned to the solventogenic portion of theprocess, and may be added to the fermentation medium in the bioreactoras a feedstock which may be converted to butanol by the fermentingmicroorganism.

In some embodiments, furfural is removed from the butanol product streamformed in the distillation process. In one embodiment, furfural isadsorbed from the butanol product stream. For example, a tertiary amineion-exchange resin or activated carbon may be used for adsorption offurfural. In another embodiment, butanol and furfural are separated bypervaporation. In a further embodiment, butanol and furfural areseparated from one another through the use of a solvent, such astriocyl-phosphine oxide (TOPO). In one embodiment, the furfural isremoved and may be sold as a chemical product.

In some embodiments, other products are removed from the butanol productstream to remove impurities from the butanol product stream andrecovered as useful products, for example, acetic acid, butyric acid,HMF, extractives.

Biobutanol produced according to the methods described herein may alsoserve as a platform molecule for the production of other compounds. Forexample, butanol may be converted into propylene, from which a widevariety of plastics and other compounds may be produced. A mixture ofbutanol, dibutyl ether (a derivative of butanol), and plant oil inspecified proportions may constitute a full performance diesel fuel. Inaddition, through well-understood chemistry involving dehydration ofbutanol followed by oligomerization through the use of a catalyst,butanol may be converted into full performance jet fuel.

Biobutanol produced according to the methods described herein may alsobe used as an intermediate chemical for producing other chemicalproducts, including but not limited to, butyl acrylate, n-butyl acetate,and glycol ethers. It may also be dehydrated to produce 1-butene, whichmay be oligomerized to produce other products, including but not limitedto, jet fuel, diesel fuel, lubricants, or alpha olefins. Butanol mayalso be used directly to produce butene derivatives. Any of thesederivatives of butanol may be produced using chemical processes that arewell known in the art.

Continuous Process

A continuous process for bioproduct, e.g., biofuel, production isprovided. In a continuous production process herein, acarbohydrate-containing feedstock is continuously pretreated to producesoluble sugar molecules, the pretreated feedstock containing solublesugar molecules is continuously fed to one or more bioreactors formicrobial production of the bioproduct, e.g., biofuel, the bioproduct iscontinuously produced by immobilized microorganism(s) in the one or morebioreactors, and bioproduct-containing effluent, i.e., fermentationbroth, is continuously withdrawn from the one or more reactors, for theduration of fermentation. In some embodiments, the feedstock iscontinuously hydrolyzed to release soluble sugar molecules. In oneembodiment, the feedstock is lignocellulosic feedstock, and ishydrolyzed with nitric acid to release soluble sugar molecules fromcellulose and hemicellulose, as described supra.

In some embodiments, the continuous process may also include downstreamcontinuous concentration and/or purification processes for recovery ofthe bioproduct, e.g., biofuel, product, wherein continuously withdrawneffluent is continuously processed in one or more concentration and/orpurification processes to produce a bioproduct.

In some embodiments, the process may also include a conditioning processto remove inhibitors of microbial growth or bioproduct, e.g., biofuel,production, as described herein. The conditioning process may operatecontinuously downstream from a feedstock hydrolysis process, andupstream from the bioreactor(s), and conditioned hydrolyzed feedstockmay be continuously fed to the bioreactor for the duration offermentation.

In some embodiments, the process may also include deconstruction of thefeedstock and/or removal of extractives from the feedstock, as describedherein. Deconstruction and/or removal of extractives may be continuousor may occur prior to or periodically throughout the continuous process.

In some embodiments, the process operates continuously for at leastabout 50, 100, 200, 300, 400, 600, 800, 1000, 1350, 1600, 2000, 2500,3000, 4000, 5000, 6000, 7000, 8000, or 8400 hours.

A “continuous” process as described herein may include periodic orintermittent partial or complete shutdowns of one or more parts of thebioproduct, e.g., biofuel, production system for processes such asmaintenance, repair, regeneration of resin, etc.

Continuous fermentation, with constant feed of hydrolyzed feedstock andwithdrawal of product-containing microbial broth, can minimize theunproductive portions of a fermentation cycle, such as lag, growth, andturnaround time, thereby reducing the capital cost, and can reduce thenumber of inoculation events, thus minimizing operational costs and riskassociated with human and process error.

The continuous methods and systems described herein can utilize one ormore, e.g., one, two, or three or more, bioreactors. When multiple (twoor more) bioreactors are used, they may be arranged in parallel, series,or a combination thereof. The bioreactors can grow the same or differentstrains of microorganism(s). The strains can be different based on thetype of sugar they metabolize to maximize bioproduct, e.g., biofuel,production. For example, a first bioreactor or multiple bioreactorsarranged in parallel, series, or a combination thereof can grow a strainthat has been selected to metabolize C5 sugars and a second bioreactoror multiple bioreactors arranged in parallel, series, or a combinationthereof can grow another strain that has been selected to metabolize C5and C6 sugars. The bioreactors are coupled to an upstream feedstockhydrolysis unit, and may also be coupled to a downstreamrecovery/separation unit. In some embodiments, the connection may beinterdigitated, such that some product separation may occur betweenprimary and/or secondary and/or further reactors in series.

A first bioreactor or multiple bioreactors arranged in parallel, series,or a combination thereof with a strain that metabolizes C5 sugars can becoupled to an upstream first stage hydrolysis module of a nitric acidhydrolysis unit for hydrolysis of lignocellulosic feedstock. A secondset of bioreactors or multiple bioreactors arranged in parallel, series,or a combination thereof with a strain that metabolizes C5 and C6 sugarscan be coupled to an upstream second stage hydrolysis module of a nitricacid hydrolysis unit for hydrolysis of a lignocellulosic feedstock.Alternatively, the same bioreactor or multiple bioreactors arranged inparallel, series, or a combination thereof may be used for conversion ofboth C5 and C6 sugars to bioproduct, e.g., biofuel. For example, bothfirst and second stage nitric acid hydrolysates of a lignocellulosicfeedstock may be added either separately or as a combined mixture to thebioreactor(s).

In some embodiments of continuous biofuel production processes andsystems described herein, butanol may be produced by a microbial strain,such as a Clostridium strain, at a titer of about or at least about 5,6, 7, 8, 10, 12, 15, 20, 25, 30, 40, 50, 60, 70, 80, or 90 g butanol perliter, or about 5 to about 90, about 5 to about 10, about 8 to about 20,about 15 to about 30, about 25 to about 50, about 40 to about 80, orabout 60 to about 90 g butanol per liter. Titer may be affected byambient conditions (e.g., pressure/temperature) and composition(acetone, salts, etc.). In some embodiments of continuous biofuelproduction processes and systems described herein, butanol may beproduced by a microbial strain, such as a Clostridium strain, with ayield of about or at least about 30, 35, 40, 50, or 60% or about 30% toabout 60%, about 40% to about 60%, or about 50% to about 60%. In someembodiments of continuous biofuel production processes and systemsdescribed herein, butanol may be produced by a microbial strain, such asa Clostridium strain, with a productivity of about or at least about 1,3, 5, 10, 15, or 20 g, butanol per liter per hour, or about 1 to about20, about 3 to about 10, about 5 to about 15, or about 10 to about 20 gbutanol per liter per hour.

In some embodiments, water saturated butanol may be skimmed off the topof the liquid or separated by equipment known in the art for theseparation of two liquid phases in the bioreactor, for furtherprocessing/product recovery operations.

System for Bioproduct Production

The invention provides a system for continuous production of abioproduct, e.g., biofuel, i.e., for conducting a continuous bioproductproduction process as described herein. The system contains a feedstockhydrolysis unit upstream from and in fluid communication with one ormore bioreactor(s). A carbon-containing feedstock is continuouslyhydrolyzed in the hydrolysis unit to produce soluble sugar molecules,and the hydrolysate is continuously fed to the bioreactor(s) as a carbonsource to support microbial growth. One or more immobilizedmicroorganism(s) in the bioreactor(s) continuously convert thehydrolysate into a bioproduct, e.g., biofuel, and bioproduct-containingeffluent is continuously withdrawn from the system.

In some embodiments, the system contains multiple bioreactors arrangedin parallel, series, or a combination thereof. In one embodiment,multiple bioreactors in parallel are all in fluid communication with asingle hydrolysis unit or multiple bioreactors in parallel are each influid communication with a different hydrolysis unit wherein thehydrolysis units are arranged in parallel and each feed a differentbioreactor, and hydrolyzed feedstock is fed continuously to eachbioreactor, with effluent continuously withdrawn from each bioreactor.In one embodiment, the system contains multiple bioreactors arranged inseries, the first bioreactor in the series is in fluid communicationwith the hydrolysis unit, and hydrolyzed feedstock is fed continuouslyto the first bioreactor in the series, with effluent continuouslywithdrawn from each bioreactor and fed to each subsequent downstreambioreactor in the series, and effluent from the last bioreactor in theseries continuously withdrawn from the system.

In some embodiments, the system for bioproduct, e.g., biofuel,production operates with the bioreactor(s) under pressure to compressgas in the bioreactor(s), including CO₂ generated by the microorganismsduring fermentation. CO₂ generated during fermentation effectivelyreduces the liquid volume in the bioreactor, thus decreasing theresidence time of the liquid hydrolyzed feedstock. Compression of gas inthe bioreactor has the effect of increasing residence time of thehydrolyzed feedstock in the reactor, which improves utilization of thesugar molecules in the feedstock and conversion of the sugar tobioproduct, e.g., biofuel, for example, butanol. Operation underpressure impacts the solubility of gaseous species (CO₂ and H₂) and mayaffect fermentation parameters of interest, such as product yield,selectivity and/or productivity, for example, by affecting the redoxpotential, pH, or other parameters. Hydrolyzed feedstock may be added tothe bioreactor continuously under pressure. The pressure in thebioreactor may be about 1 to about 30 atm, or about or at least about 1,2, 3, 5, 10, 15, 20, 25, or 30 atm. Alternatively, CO₂ may be removedperiodically, intermittently, or continuously from the bioreactor, forexample, at points along the length of the bioreactor. Fermentationgases may also be removed between reactor stages (e.g., primary and/orsecondary and/or further reactors in series). In a further embodiment,residence time of the hydrolyzed feedstock may be increased by using asolid support with hydroscopic properties to increase liquid holdup, andthus increase residence time. Both productivity (g bioproduct, e.g.,biofuel, per hour per liter) and titer (g bioproduct, e.g., biofuel, perliter) may be increased as a result of the increased residence time ofhydrolyzed feedstock in the bioreactor.

In some embodiments, the system may also include downstream continuousconcentration and/or purification modules for recovery of thebioproduct, e.g., biofuel, product, for processing of continuouslywithdrawn effluent to produce a bioproduct. In some embodiments, thesystem includes a module for concentration of the bioproduct-containingeffluent, in fluid communication with and downstream from thebioreactor(s). In one embodiment, concentration includes distillation.In one embodiment, distillation comprises MVR. In a further embodiment,the system includes a module for purification of bioproduct, e.g.,biofuel, from the concentrated bioproduct-containing effluent, in fluidcommunication with and downstream from the concentration module. In oneembodiment, purification includes distillation.

In some embodiments, the system may also include a conditioning unit forremoval of inhibitors of microbial growth or bioproduct, e.g., biofuel,production, as described herein. The conditioning unit may operatecontinuously downstream from and in fluid communication with thefeedstock hydrolysis process, and upstream and in fluid communicationwith the bioreactor(s), and conditioned hydrolyzed feedstock may becontinuously fed to the bioreactor for the duration of fermentation. Inone embodiment, the conditioning unit includes ion exchange resin, andthe inhibitors are retained on the resin. In another embodiment, theconditioning unit includes a precipitation unit and the inhibitors areremoved with the separated precipitate. In a further embodiment,inhibitory compounds are separated from the hydrolysate in a steamstripping operation.

In some embodiments, the system may also include units fordeconstruction of the feedstock and/or removal of extractives from thefeedstock, as described herein. Deconstruction and/or removal ofextractives may operate continuously upstream and in fluid communicationwith the hydrolysis unit, or may occur prior to or periodicallythroughout the continuous process.

Energy Integration

The bioproduct, e.g., biofuel, production processes and systemsdescribed herein may include one or more energy integration systems, forcapturing and recycling energy generated in one part of the bioproductproduction process and using the captured energy to drive another partof the process. The energy integration schemes described herein includeintegration between process areas and effect a global change to theoverall plant energy use.

Methods of energy exchange are well known in the art, for example, feedbottoms exchangers for distillation towers. Heat exchange methods mayalso be used at various points in the system.

In one embodiment in which a two stage nitric acid hydrolysis process isused for hydrolysis of a lignocellulosic feedstock, as described supra,flash steam generated in the first stage and/or second stage hydrolysisprocess(es) may be captured and used for deconstruction of the feedstockprior to hydrolysis.

In one embodiment in which a two stage nitric acid hydrolysis process isused for hydrolysis of a lignocellulosic feedstock, as described supra,flash steam generated in the second stage hydrolysis process may berecompressed and the recompressed steam used to provide energy for thefirst stage hydrolysis. In one embodiment, the flash stream is notcompressed.

In one embodiment in which a two stage nitric acid hydrolysis process isused for hydrolysis of a lignocellulosic feedstock, as described supra,flash steam generated as part of the hydrolysis process may be used toprovide lie steam for steam stripping operations, to preheat streams,remove inhibitory compounds from hydrolysate, and/or to facilitateproduct separation and recovery operations.

In one embodiment in which a two stage nitric acid hydrolysis process isinitially used for hydrolysis of a lignocellulosic feedstock, asdescribed supra, flash steam is generated in the second stage hydrolysisprocess may be used to provide energy for a third stage hydrolysis, withthe temperature of the third stage lower than the temperature of thesecond stage, and with the temperature and/or residence time of thesecond stage reduced in comparison to a process without the third stage,thus permitting hydrolysis of remaining oligomeric sugar molecules withless degradation than hydrolysis performed at a higher temperature thanthe temperature of the third stage. This method could also be extendedto four or more stages of hydrolysis with decreasing temperature in acascade effect. In one embodiment with three hydrolysis stages, flashsteam generated in the second stage is used to provide energy for thefirst stage, and flash steam generated in the first stage is used toprovide energy for the third stage.

In one embodiment in which a two stage nitric acid hydrolysis process isused for hydrolysis of a lignocellulosic feedstock, as described supra,flash steam generated in the first and/or second stage hydrolysisprocess may be recompressed and the recompressed steam is used toprovide energy for a distillation process for purification ofbioproduct, e.g., biofuel, from bioproduct containing effluent fromcontinuous microbial fermentation, as described supra.

In one embodiment in which a two stage nitric acid hydrolysis process isused for hydrolysis of a lignocellulosic feedstock, as described supra,flash steam generated in the first and/or second stage hydrolysisprocess may be used to provided energy for preheating a feed stream to adistillation process for purification of bioproduct, e.g., biofuel, frombioproduct containing effluent from continuous microbial fermentation,as described supra. The flash steam may optionally be recompressed priorto use for preheating the feed stream.

In one embodiment in which a two stage nitric acid hydrolysis process isused for hydrolysis of a lignocellulosic feedstock, as described supra,flash steam generated in the first and/or second stage hydrolysisprocess may be recompressed and the recompressed steam is used toprovide energy for drying and/or dehydration of products separated in adistillation process as described supra. For example, the recompressedsteam may be used to provide energy for drying and/or dehydration ofbiomass from the fermentation process.

In some embodiments, lignin is recovered in the solids-containingresidue remaining after hydrolysis of lignocellulosic feedstock, forexample, in the solids-containing residue remaining after the secondstage of a two stage nitric acid hydrolysis process, as described supra.The lignin-containing residue may be used as an energy source for thebioproduct, e.g., biofuel, production process, as a fuel source forelectricity generation, as a feedstock for chemical production, forexample, production of phenolic resins, and/or as a soil enhancer.

Integrated Bioproduct Production Plant

An integrated plant is provided that can produce a bioproduct, such as abiofuel. For example, biobutanol may be produced from a wide variety offeedstocks in a capital and energy efficient process, with lowgreenhouse gas (GHG) emissions and the potential to make a significantcontribution to reducing oil imports, achieving advanced biofuelstargets, developing a domestic bioindustry, creating jobs, and promotingeconomic development. Embodiments of such an integrated biofuel, e.g.,biobutanol, plant, utilizing processes and systems for continuousbiofuel production described herein, are schematically depicted in FIGS.1-3.

A biorefinery as described herein may provide an economic benefit, theproduction of bioproducts with a reduced carbon intensity (emission,footprint) as compared to petrochemically derived counterparts. Theprimary driver for this reduction in carbon intensity is the relativelyrapid utilization of carbon in the feedstock as compared to petroleumbased chemical feedstocks. As an example of the reduction of carbonintensity, n-butanol is the bioproduct and the bioproduct is used todisplace gasoline use. The carbon intensity of gasoline depends on thefeedstock source of production, production energy, producttransportation and product use and is approximately 0.095 kg CO₂e/MJ ofgasoline. Similarly, butanol produced in such a biorefinery as describedherein has a carbon intensity of approximately 0.010 kg CO₂e/MJ ofbutanol. The carbon intensity of the biorefinery also depends on thefeedstock source of production, production energy, producttransportation and product use. In the case where reduction in intensityis largely attributed to a feedstock, CO₂ uptake credit is generated asthe biomass is produced prior to harvest.

The avoidance of carbon intensity has been valued by commodity agenciessuch as the Chicago Board of Trade. A price target is subject to marketdemand and is priced accordingly. As an example, at $10/MT CO₂e, or$0.01/kg CO₂e avoided, a production facility that generated 1e9 MJ ofbutanol which was used to displace gasoline would result in an avoidanceof 8.5e7 kg CO₂e, with a value of $0.85 MM.

An integrated bioproduct, e.g., biofuel, plant can be built to a varietyof capacities. In some instances, a pilot plant has the capacity toprocess one to five dry tonne(s) of feedstock per day. The feedstock forthe plant can be cellulosic biomass, for example, lignocellulosicbiomass such as woody biomass, which may be sourced locally and isavailable in many regions of the country. Pretreatment of the biomasscan be accomplished an acid hydrolysis process, such as a two stagedilute acid process to extract soluble sugars from the hemicellulose andcellulose.

In some embodiments, these sugars can be fermented to biofuel, e.g.,biobutanol, using Clostridium strains. In some embodiments, aClostridium strain can produce n-butanol from both monomeric andmultimeric forms of both C5 and C6 sugars. Fermentation can occur in animmobilized bed bioreactor running a continuous process, which candeliver up to or more than ten times the productivity of acomparably-sized batch fermentor. Product recovery and distillation (forexample, high-efficiency mechanical vapor compression) techniques andadvanced integration of heat streams from adjacent process streams andareas to produce high purity biofuel, e.g., biobutanol with low overallenergy use.

The integrated bioproduct, e.g., biofuel, production plant can be afully integrated standalone facility. In addition to the operationscontained in the integrated plant, the facilities can include feedstockstorage and handling, product storage and loadout, and on-siteutilities. The integrated plant can have one or more streams to recoverheat and/or materials. For example, recycle streams can be used toimprove efficiency of separation processes or bioconversion processes.Other streams can be used for heat exchange from one process unit toanother, or within a process unit.

In some embodiments, an integrated bioproduct, e.g., biofuel, productionplant may be co-located to utilize a waste stream, such as hemicellulosefrom a pulp mill, to achieve economic advantages gained throughco-location and co-utilization of utilities, feed handling, feedlogistics, off-take, chemical production, etc.

In various embodiments, the bioproduct, e.g., biofuel, production plantcan utilize one or more hydrolysis stages for feedstock preparation, oneor more conditioning processes to prepare hydrolysates forbioconversion, one or more fermentors for growing one or more strainsthat are capable of producing a bioproduct such as butanol andoptionally other products of interest, and one or more separationprocesses to isolate the desired products. The various processing unitscan be designed and coordinated such that the complete operation of theplant is in a continuous manner. Accumulation of products or feedmaterials between process operations can be avoided. Residence time ofprocessed materials prior to being fed to a downstream operation can bereduced to avoid undesirable degradation or modification of materials.Rates of processing for upstream processing units can be controlledbased on performance of downstream processing units and vice-versa. Forexample, if a reduction in bioconversion by a microbial strain isobserved, the rate of hydrolysis of a feedstock can be reduced such thataccumulation of products is avoided.

In some embodiments, commercial plant output can include butanol as theprimary product, acetone, a mixed solvent containing acetone, ethanoland sugar degradation products, and lignin. Per tonne of a particularfeedstock, the plant can produce about or at least about 53.5 gallons ofbutanol, 4.1 gallons of acetone, 0.039 tonnes of mixed solvents and0.419 tonnes of a lignin. The butanol and acetone can be sold into thefuels and chemicals markets, respectively. The mixed solvents (which mayinclude acetone, ethanol, butanol, degradation products, woody biomasscompounds, fermentation byproducts, fermentation generated biomass,and/or water) and most of the lignin can be used in an onsiteco-generation unit to generate all of the steam and electricity requiredto operate the plant, and the remaining lignin can be dried to removewater, for example to about 15% moisture content, and sold as boilerfuel. The removal of water from the lignin is important to increase thevalue of the lignin stream in that the energy content per unit weight isincreased by removing the water and the commensurate latent heat of thewater. Drying techniques are well known in the art.

An integrated biobutanol plant can produce butanol at a variety ofscales. Butanol can be produced at pilot scale at about 13,000 gallonsper year, at demonstration scale at about 2 to 2.5 million gallons peryear (consuming about 150 tonnes of feedstock per day) and at commercialscale at about 50 million gallons per year.

For every gallon of biobutanol produced, the plant can produce about orat least about 0.08 gallons of acetone and about or at least about 2.7kg of lignin. The estimated feedstock consumption of the commercialplant can be about 2,700 dry tonnes per day (112,500 dry kg/hr), basedon a yield of 53 gallons of biobutanol per tonne of feedstock.

The amount of butanol that can be produced per tonne of feedstock can beabout, up to about or at least about 10, 20, 30, 40, 50, 60, 70, or 80gallons. A petroleum analysis indicates a displacement of 2.7 millionequivalent barrels of oil annually for a 50 million gallon per yearfacility. The plant can be located in numerous areas in the countrywhere this amount of forest waste, with sufficient surplus to avoidmarket pressure, is available locally. The plant can include all of theunit operations of the feedstock bioconversion, plus feedstock handlingand product distribution and load out operations. In addition, thecommercial facility can have its own biomass-fired power plant on site,which can use lignin in the solids-containing residue remaining afterfeedstock hydrolysis, the small amount of ethanol and a portion of theacetone produced in the fermentation process recovered in thedistillation system, plus furfural and HMF extracted from the feedstockto provide all of the steam and electricity required by the process,with excess lignin sold to offsite power facilities. The facility mayrequire about or at least about 20,000, 30,000, 40,000, 50,000, 60,000,70,000, 80,000, 90,000, 100,000, 150,000, 200,000, 250,000, 300,000,350,000, 400,000, 450,000, or 500,000 BTUs of thermal energy per gallonof butanol, about or at least about 1, 1.5, 2, 2.5, 3, 3.5, 4, 5, or 10kilowatt hours per gallon and about or at least about 1, 2, 3, 4, 5, 6,7, 8, 10, 20, or 30 gallons of water per gallon of biobutanol produced,depending on the process configuration. These numbers can be reduced,including further reductions in the estimated water usage. For example,air coolers can be used whenever possible to reduce cooling towerevaporative losses and minimize the fresh water footprint.

The equipment for an integrated bioproduct production plant as describedherein can be purchased from commercial manufacturers of industrialprocess equipment. The equipment materials can be selected based oncorrosion and erosion resistance. In particular, the equipment materialscan be evaluated for the hydrolysis processes, which may be performedunder acidic conditions at elevated temperatures and pressures. In someembodiments, the equipment design does not require the use of exoticmaterials or specialized equipment available from a single or limitednumber of vendors. Notably, in embodiments in which a nitric acidhydrolysis process is used, pretreatment vessels can be made ofstainless steel (e.g., Duplex 2205) rather than the expensive alloysoften required in other processes. Spare parts can be kept at the plantto ensure continuous processing without a lengthy interruption orturnaround.

Operating parameters and behavior of fermentors including inoculation,longevity of growth, pH control, and sterilization can be determined atlab bench or pilot scale prior to implementation at commercial scale. Insome embodiments, variability can be addressed by segregating C5 and C6fermentor volumes into multiple vessels, for example, two, three, ormore vessels per unit operation. This design concept can allow maximumflexibility as the vessels can be manifolded to allow isolation orrecirculation of media by individual reactor. This operationalflexibility can allow run times to be extended by rotating the positionof the individual fermentors within the train while optimizingmicrobial, e.g., Clostridium performance. Individual reactors can beisolated, sterilized, and inoculated while the remaining vessels areonline. The bioreactor design and operational configurations, which caninclude multiple reactors in series, can be chosen to maximize theproduction of the bioproduct of interest, for example, a biofuel, e.g.,biobutanol, thereby reducing capital costs and improving operationallogistics.

An integrated bioproduct, for example, biofuel, e.g., biobutanolproduction plant can include a high degree of instrumentation andcontrol using a supervisory control and data acquisition (SCADA) systemand/or distributed control system (DCS). These systems collect real timedata on a wide range of performance parameters and the data may be usedto optimize process control parameters, setpoints, and conditions. Forexample, a custom designed SCADA system can collect multiple parametersincluding fermentor offgas concentration data measured by an online MS,which can be an effective real-time indicator of metabolism andoptionally solvent production in embodiments in which a solvent such asbiobutanol is produced.

A variety of products can be produced using the systems and methodsdescribed herein. These products include butanol, acetone, ethanol,green gasoline, and mixed alcohols. Other products include lignin,cellulose, hemicellulose, sugars, acids, or any other product describedherein. Natural products such as xylitol, vitamin B12, and othercompounds may be separated in the production process to improve planteconomics. Organic products that can be used as a fuel can be blendedwith each other, or blended with additional materials. For example,butanol can be blended with gasoline or any other combustible fuel.

Butanol produced by the systems and methods described herein, includingfermentation and separation, can be at a purity of about or at leastabout 30, 40, 50, 60, 70, 75, 80, 85, 90, 95, 97, 99, 99.5, 99.8, 99.9,or 99.99%. Acetone produced by the systems and methods described herein,including fermentation and separation, can be at a purity of about or atleast about 30, 40, 50, 60, 70, 75, 80, 85, 90, 95, 97, 99, 99.5, 99.8,99.9, or 99.99%. Ethanol produced by the systems and methods describedherein, including fermentation and separation, can be at a purity ofabout, up to about, or greater than about 30, 40, 50, 60, 70, 75, 80,85, 90, 95, 97, 99, 99.5, 99.8, 99.9, or 99.99%.

Butanol produced by the systems and methods described herein, afterfermentation or separation, can be a blend of butanol, acetone, andethanol. In one embodiment, the blend can be 70 parts butanol to 30parts acetone. This can be determined on an organic solvent basis,excluding water. In other embodiments, the blend can includebutanol:acetone:ethanol at a ratio of 33:12:1, 58:12:1, or 90:9:1.

Butanol production for a commercial plant can be about 50 milliongallons of butanol per year. In some embodiments, a plant may bedesigned to produce less than about 1 million gallons per year ofbutanol, or about 1 to about 2, about 2 to about 5, about 5 to about 10,about 10 to about 50, about 20 to about 50, about 30 to about 50, about40 to about 50, or about 45 to about 50 million gallons per year ofbutanol.

Lignin separated in an integrated bioproduct production plant asdescribed herein, in the form of lignin-containing residue remainingafter hydrolysis of lignocellulosic feedstock, can be stored orprocessed by a lignin handling and storage unit. For example, this unitoperation can process the lignin-containing residual material from thesecond stage acid hydrolysis of lignocellulosic feedstock, as describedsupra, including unconverted cellulose and hemicellulose material. Thelignin product stream can be dried, for example, using hydrolysis flashsteam. At about 35 wt % moisture, the material will have a usableheating value. The material can be further dried to improve the productvalue, for example, to about 15 wt % moisture, subsequently pelletized,and stored for sale as fuel, for example, for electricity generation orburned as dried to provide thermal energy. Dried, pelletized lignin mayalso be used to generate high pressure steam to provide energy for usein first and second stage nitric acid hydrolysis processes forhydrolysis of lignocellulosic feedstock, as described supra.

In some embodiments, biomass can be removed from the fermentation brothduring the product separation and distillation phase. The recoveredmaterial can be dried and burned for process heat or can be digested togenerate methane and remove the cellular mass without release to theenvironment.

The effluent streams from a nitric acid pretreatment process can containsignificant levels of nitrogen. Ammonium nitrate created duringneutralization of nitric acid can be converted to nitrogen and water.Ammonium nitrate containing solutions may also be used as feedstocks forsubsequent microbial water treatment ponds.

The following examples are intended to illustrate, but not limit, theinvention.

EXAMPLES Example 1 Butanol Production in Continuous Packed BedBioreactors

Clostridium strains were grown in 100 mL or 1 L continuous packed bedbioreactors for lengths of time as shown in Table 1. Co-7449 is a strainof Clostridium saccharobutylicum that is very stable in continuousculture, possesses increased acid recycle capabilities in comparison towild-type, and utilizes mixed sugars in a softwood hydrolysate well.Co-5673, an environmental isolate of Clostridium, is also stable incontinuous culture, and possesses increased tolerance to acids. Themicrobial cells were grown anaerobically on bone char, using a sugarsubstrate. Butanol titer, yield, and performance are included in Table1, calculated using the best sustained performance (100 hours or more)for each fermentation. Substrate concentrations in the table areexpressed as weight of substrate per volume of liquid. Data fromrepresentative fermentation runs is presented in FIGS. 6-12.

TABLE 1 Total Bioreactor EFT* Butanol Y_(BuOH) P_(BuOH) Run No. volume(h) Strain Substrate (g/L) (% theor) (g/L/h) 2008065  100 mL 1024Co-7449 4% Glucose 4.2 49 3.1 2008137 1000 mL 831 Co-7449 4% Sucrose 7.561 5.1 2009012 1000 mL 478 Co-5673 5% Sucrose 8.4 63 6.1 2009021 1000 mL473 Co-7449 4% Xylose 5.4 63 4.1 2009023 1000 mL 568 Co-5673 4% Xylose4.0 63 3.0 2009047 1000 mL 1250 Co-7449 4% Xylose 4.7 88 3.4 20090541000 mL 352 Co-7449 4% Mixed sugar 5.6 61 4.0 simulated hydrolysate**2009057 1000 mL 628 Co-5673 4% 5.9 61 4.3 Mixed sugar simulatedhydrolysate 2009060 1000 mL 640 Co-7449 4% 5.0 56 3.6 Mixed sugarsimulated hydrolysate *EFT = elapsed fermentation time **Mixed sugarsimulated hydrolysate = 5 parts mannose (31%), 4 parts xylose (27%), 3parts glucose (16.5%), 2 parts galactose (12%), 2 parts arabinose (11%)

Example 2 Continuous Biobutanol Production and Recovery

A continuous biobutanol production and recovery process is describedbelow, with all of the described component processes (e.g., feedstockhydrolysis, fermentation, recovery of product) operating simultaneouslyand continuously in an integrated biobutanol production plant.

Hydrolysis of Lignocellulosic Feedstock

C5 and C6 sugars are produced from hemicelluloses and cellulosecomponents of wood chips in a two-stage dilute nitric acid hydrolysisprocess. The two-stage approach includes two reaction stages at twodifferent temperatures, minimizes thermal degradation products andmaximizes sugar recovery from both the hemicelluloses and cellulosecomponents of the feedstock.

First Stage Hydrolysis

Wood chips are mixed with nitric acid and water and pressured into thefirst stage hydrolysis reactor using a progressive reducing screw auger.The first stage hydrolysis reactor operates at or around 175° C. using115 psig steam and is sized to provide a residence time of 5 to 9minutes. A discharge auger and blow valve deliver reactor effluent to aflash tank where low pressure steam is recovered for re-use in theprocess. The steam may be augmented by recovered steam from otheroperations.

C5 hydrolysate is separated from the unconverted biomass in a screwpress, stripped with nitrogen for oxygen removal, and pumped to the C5fermentation section of the biobutanol production plant. (Despitecontaining both C5 and C6 sugars, the stage 1 hydrolysate liquorcontains nearly all of the C5 sugars, and as a matter of nomenclaturehas been termed “C5 hdyrolysate” herein.) The C5 hydrolysate is broughtto about pH 3.5 with ammonium hydroxide and passed through an anionexchange resin bed upstream of fermentation. The screw press may includea solids wash step to maximize recovery of fermentable sugars.

Second Stage Hydrolysis

Residual uncoverted biomass from the first stage hydrolysis is mixedwith nitric acid and water and pressured into the second stagehydrolysis reactor using a progressive reducing screw auger. The secondstage hydrolysis utilizes a higher temperature than the first stagehydrolysis to break down the recalcitrant cellulose component.

The second stage reactor operates by injecting saturated live steam at215° C. (with the relationship between temperature and pressure wellknown by those of skill in the art) and is sized to provide a residencetime of 3-8 minutes. A discharge auger is used to deliver reactoreffluent to a flash tank where additional low pressure steam isrecovered.

The C6 hydrolysate is separated from solids containing unconvertedcellulose and lignin in a screw press, stripped with nitrogen for oxygenremoval, evaporated to remove water and some acetic acid, brought toabout pH 3.5 with ammonium hydroxide, passed through an anion exchangeresin bed (e.g., Duolite A7), and pumped to the C6 fermentation sectionof the biobutanol production plant. The screw press separation alsocontains a solids wash step to maximize recovery of fermentable sugars.Residual cellulose/lignin is either neutralized and disposed of or steamdried and utilized as boiler fuel for process steam and/or electricitygeneration.

C5 Fermentation

Neutralized C5 hydrolysate from the first stage hydrolysis unitoperation is cooled to fermentation temperature, treated to removefermentation inhibitors via anion exchange as discussed above, mixedwith nutrients and charged to a bioreactor or the first bioreactor in aseries of bioreactors. The C5 hydrolysate is fermented into biobutanolin the bioreactor using an immobilized Clostridium strain that has beenselected to maximize titer, yield, and butanol selectivity for C5hydrolysate.

The fermentation process also produces fermentation off gas, primarilycarbon dioxide and hydrogen, which strips some solvent from thebioreactor. All three reactors operate near atmospheric pressure andinclude a heating/cooling jacket to maintain temperature at 32° C. Eachof the reactors includes a controlled nitrogen purge into the vaporspace that is sampled and vented to a vent gas treatment unit operationalong with fermentation off gas.

The fermentation is carried out in a temperature controlled bioreactorunder anaerobic conditions after supplementing the hydrolysate withnutrients for growth of the microorganism. After colonization of thebioreactor by the microorganism is achieved, a continuous feed ofsupplemented hydrolysate is started together with the simultaneouscontinuous withdrawal of the same amount of fermentation broth.

C6 Fermentation

Neutralized C6 hydrolysate from the second stage hydrolysis unitoperation is cooled to fermentation temperature, treated to removefermentation inhibitors via anion exchange as discussed above, mixedwith nutrients and charged to a separate bioreactor or a series ofbioreactors. The C6 fermentation unit operation is nearly identical tothe C5 fermentation, discussed above, with the exception that thespecific strain of Clostridium has been optimized to maximize titer,yield, and butanol selectivity for C6 hydrolysate. Alternatively, thesame strain is used for both C5 and C6 fermentations in the same orseparate bioreactors.

Product Concentration

Reactor effluent from the C5 and C6 fermentations is combined into aproduct recovery feed tank (or “harvest tank”) where fermentationcontinues before being fed to the product recovery distillation columnfeed tank. Fermentor effluent is pumped from the feed tank to thedistillation column where the dilute product stream is concentrated, forexample from about 2.5 wt % total organics in the feed to about 50 wt %in the overhead liquid product or from about 1 wt % total organics toabout 35 wt % in the overhead liquid product.

Overhead vapor from the distillation column is condensed in the overheadcondensor. The recovered bottoms stream is passed through a heatexchanger, where energy is exchanged with the column feed stream torecover energy. The overhead stream is pumped to additional separationequipment for further purification of separate biofuel products, forexample, acetone, butanol, and ethanol.

Product Distillation

Organic products are further purified from the concentrate bydistillation. For example, high purity butanol and acetone may beproduced with some ethanol removed via a side draw.

Example 3 Two-Stage Nitric Acid Hydrolysis of Lignocellulosic Feedstockin a Batch Reactor

Nitric acid hydrolysis of a lignocellulosic feedstock was performed intwo stages. The feedstock was beetle killed lodgepole pine obtainedthrough Renewable Fiber in Fort Lupton, Colo. Three quarter inch woodchips were milled to pass through a′/4 inch screen.

Approximately 1.3% nitric acid on a dry wood basis was reacted withfeedstock in a 1.9 L reactor. The milled ¼ inch wood chips were loadedinto a five gallon bucket and charged with water and nitric acid. Thenitric acid concentration was approximately 1.3% on a dry wood basis andwater was added to the bucket to completely submerge the wood chips. Thetotal solids loading of the mixture was approximately 12 wt %, whichcorresponded to a liquids to solids ratio of approximately 7.5. Thebucket was then sealed and placed on rollers where the contents of thebucket mixed for approximately 30 minutes. This step was done toimpregnate the acid into the wood chips. The contents of the bucket werethen transferred to the 1.9 L reactor, where the hydrolysis reactiontook place. The reactor was sealed and charged with steam in order toreach a reaction temperature of 175° C. The time that the contents ofthe reactants were at this temperature was approximately 7 minutes,after which the contents of the reactor were flashed into a vessel atatmospheric pressure with additional cooling to rapidly cool thematerial and stop the hydrolysis reaction. The pH of the solution wasapproximately 2 during the reaction.

The reaction mixture was separated using a vacuum filtration unit intofirst stage hydrolysate and solid residue. The first stage hydrolysatewas analyzed for conversion of cellulose and hemicellulose to solublesugar molecules using high performance liquid chromatography (HPLC). Theyields of soluble sugars based on cellulose and hemicellulose conversionwere calculated by measuring sugars produced from complete hydrolysis ofcellulose and hemicellulose concentrations in the starting material.Concentrated acid was used to hydrolyze both the cellulose andhemicellulose fractions of the wood. A theoretical maximum amount ofsugar was then calculated based on the conversion of cellulose andhemicellulose to sugars. The yield from the dilute nitric acidhydrolysis was then compared to the theoretical maximum. In the firststage nitric acid hydrolysis reaction, 15.8% of hydrolyzed cellulose wasdetected as soluble sugars (glucose and oligomers) and 71.1% ofhydrolyzed hemicellulose was detected as soluble sugars (xylose,mannose, and other oligomers) in the first stage hydrolysis reaction.

The solid residue from the first stage hydrolysis was rinsed with waterto remove residual soluble sugars from the solids and to minimize theamount of sugar degradation in the second stage hydrolysis reaction. Anitric acid concentration of approximately 1.3 wt % on a dry solidsbasis was used to for hydrolysis of the solid residue. The residualsolids were contacting with acid in a rolling bucket for approximately30 minutes, as described above. The solids loading was approximately 14wt %, or a ratio of about 6.5 liquid to solids. The acid impregnatedresidual material was then transferred to the 1.9 L reactor and injectedwith steam. The operating temperature of the second stage hydrolysisreaction was approximately 220° C. The contents in the reactor wereheated to 220° C. for approximately 4.5 minutes and then flashed into aflash vessel to rapidly cool the reactants and stop the reaction. The pHof the solution was approximately 2 during the reaction.

The reaction mixture was separated into second stage hydrolysate andresidual biomass using a vacuum filtration process. The second stagehydrolysate was analyzed for conversion of cellulose and hemicelluloseto soluble sugar molecules, as described above. 23% of hydrolyzedcellulose was detected as soluble sugars (glucose and oligomers) and 0%of hydrolyzed hemicellulose was detected as soluble sugars (xylose,mannose, and other oligomers) in the second stage hydrolysis reaction.

Example 4 Conditioning of Hydrolyzed Feedstock with Ion Exchange Resin

First stage nitric acid hydrolysate from beetle killed lodgepole pine,prepared as described in Example 3, was conditioned to remove inhibitorsof microbial growth by passage through an anion exchange column. DuoliteA7 resin was used for conditioning of the first stage hydrolysate. Theanion exchange resin was prepared using a 1 M solution of sodiumhydroxide and then rinsed with distilled water.

The first stage hydrolysate, with a sugar concentration of approximately50 g/L, was brought to room temperature and then to pH 5.5 usingammonium hydroxide, and was then applied to the prepared ion exchangecolumn. Hydrolysate that passed through the column was used as a feedfor microbial fermentation, and microbial growth was assessed, incomparison with hydrolysate that had not passed through the column.Fifteen milliliter fractions were eluted from the ion exchange columnand were collected, 10 ml of which were then used as a fermentation feedto test for microbial growth. The remaining 5 ml in each fraction wasanalyzed for sugar concentration and presence of phenolic compounds.

Nutrients were added to the wood hydrolysate fractions and filtered witha 0.2 m filter to sterilize the media before inoculation. The filteredmedia was then inoculated with Clostridium strain Co-7449. Thefermentations were inspected for growth over a 72 hour time frame. Therewas a clear point at which the bacteria stopped growing and that pointrepresents a breakthrough of unidentified compounds in the ion exchangecolumn.

Effluents from the fermentations with conditioned and unconditionedhydrolysate were analyzed by HPLC. Based on the HPLC analysis, anincrease in an unidentified peak correlates well with the inhibitedgrowth that was observed with the microorganism. Therefore, this peakmay have played a role in the toxicity of the hydrolysate. Based on theresidence time in the HPLC column, the peak is believed to contain aphenolic compound that is strongly related to toxicity. Duolite A7 is aphenolic based anion exchange resin, so it is possible that thepostulated phenolic inhibitor compound was retained on the resin due tohydrophobic interaction with phenolic groups on the resin. It was alsonoted that the ion exchange process resulted in a loss of sugar in thehydrolysate. The amount of sugar loss was approximately less than 10% ofthe initial concentration.

A larger batch slurry process with Duolite A7 resin was used forevaluation of effect of conditioned hydrolysate on butanol titer andyield. The butanol titer and yield on the conditioned hydrolysate were7.7 g/L and 0.17 g/g sugars converted, respectively. The microorganismdid not grow on the unconditioned hydrolysate. The results of HPLCanalysis are shown in FIG. 5.

Example 5 Continuous Fermentation of Clostridium Immobilized in a 110Liter Packed Bed Bioreactor for 350 Hours

Clostridium saccharobutylicum Co-7449 (PCT/US09/40050) was grownanaerobically in a packed bed bioreactor with 110 L nominal volume and63.7 L working volume. The L/D ratio of the bioreactor was 8.

The Clostridium was immobilized on bonechar. The bonechar particles hada size of 3000 to 5000 microns, with a bulk density of about 0.72/ml.About 100 pounds of bonechar was loaded into the reactor. Immobilizationwas achieved by first filling the reactor with about 40 L of CP3 mediawith 4% sucrose and then adding to the reactor 20 L of Clostridium broththat had an OD at 600 nm of about 1, and recalculating the contents ofthe reactor for 24 hours.

The growth medium was essentially identical to P2 medium, as describedin Jesse et al. (2002) Journal of Industrial Microbiology andBiotechnology 29:117-123, with 4% sucrose as carbohydrate feed.

Continuous culture was achieved after the bioreactor had been inoculatedby pumping the growth media at a constant rate into the bottom of thebioreactor and continuously removing broth from the top of thebioreactor in order to maintain a constant liquid level in thebioreactor. Continuous fermentation continued for 350 hours.

The feed rate for the run was initially 800 g/min, was reduced to 400g/min at about 60 hours, and was increased to 500 g/min at about 143hours. The average pH was about 4.95 and the average pressure was about3.24 psi. N2 was added at a rate of 0.7 L/min for the duration of thefermentation. The average butanol titer, productivity, and yield were3.44 g butanol/L, 1.55 g butanol/L/hr, and 0.172 g butanol/g sucrose,respectively.

Example 6 Conditioning of Hydrolyzed Feedstock with Metal Salts

A hydrolysate was prepared from beetle killed Lodgepole pine usingnitric acid as the catalyst for the hydrolysis reaction. The followingconditions were used for hydrolysis: nitric acid concentration 0.4-0.5%on a dry wood basis, pH approximately 1.9-2.2, temperature 170° C., time7 minutes, approximately 25-30% solids in the feed.

The raw hydrolysate was measured out into 100 ml glass bottles tovolumes of 50 ml using a pipette. The pH of the hydrolysate samples wasthen adjusted to pH values in the range of 5.5 to 10 with a 15% solutionof ammonium hydroxide.

Aluminum sulfate and ferric chloride were added at concentrations in therange of 3 g/L to 5 g/L and the solutions incubated for about 30 minutesat temperatures in the range of 20° C. to 40° C. The solutions weremixed during the incubation using a magnetic stir plate. The solutionswere then filtered through a 0.2 micron filter to separate precipitatefrom the liquid hydrolysate.

The solutions were then cooled to room temperature if not already atroom temperature. The pH of the solutions was then adjusted to 7.2 withnitric acid or ammonium hydroxide. After pH adjustment, 10 ml of eachsolution was then filtered through a Pall sterile syringe filter with apore size of 0.2 microns into a 15 ml falcon tube. The solutions werethen placed in an anaerobic hood overnight to de-oxygenate.

Media components were added to the de-oxygenated hydrolysate solution atthe prescribed concentrations to support microbial growth (i.e., growthmedia components and trace elements). The tubes were then inoculatedwith a butanol-producing Clostridium strain at a concentration ofapproximately 5×10⁷ CFU. The conditions used for fermentation were asfollows: volume 10 ml, pH approximately 6.8 before inoculation,temperature 30° C.

Aluminum sulfate and ferric chloride were both successful intransforming an otherwise un-fermentable hydrolysate into a fermentablefeedstock that supported microbial growth and production of butanol.Under the conditions used for fermentation, aluminum sulfate produced afeedstock that resulted in higher butanol production along with lessprecipitate in the final product than ferric chloride. The best resultsfor treatment of raw hydrolysate with aluminum sulfate and ferricchloride were at the following conditions: metal salt concentration 3g/L, pH 9.5, room temperature (about 20° C.). The butanol concentrationsafter microbial fermentation for 72 hours were 8.64 g/L and 7.69 g/L foraluminum sulfate and ferric chloride, respectively.

Adjustment of hydrolysate pH before metal salt addition was found to beimportant. For example, a solution adjusted to pH 9 before addition ofmetal salts did not ultimately support microbial growth. However,adjustment of the solution to pH 9.5 resulted in a conditionedhydrolysate in which the microorganism grew and produced butanol.

Lower temperatures also resulted in lower sugar loss. At roomtemperature, the sugar loss was only 6%.

Example 7 Hemicellulose Extraction from Wood Chips with Deconstructionof Residual Cellulose

Grey stage Lodgepole pine chips, moisture content approximately 24.9%,were screened for debris and passed through a thermomechanicaldisintegrator in order to ensure (1) adequate acid impregnationthroughout the chip for the liberation of hemicellulosic sugars, and (2)to remove some wood extractives.

The disintegrator was a Bauer/Andritz RT Impressifiner, used under thefollowing conditions. Some dilution water was added to saturate the woodchips, steam was added at a delivery pressure of 1.38 bar, residencetime was 20 seconds, and the flow restriction at the exit of the RTImpressifiner was set to 1 inch.

A sample of the preliminary pressate was collected. 1.42% (w/w) nitricacid was added to the solid material at the exit of the RT Impressifinerand resulted in a 32-37% (w/w) solids stream. The material was collectedin drums, stored at about 10° C. for processing 12-18 hours later. Thetemperature of the material at the exit of the disintegrator was 60° C.,and cooled about 15-20° C. in 15 hours.

The acid impregnated material was then added to a feed hopper for adigestor feeding system. The digestor was a continuous feed, pressurerated, screw conveyor vessel operated nominally at 7.92-6.13 bar (90-110psig), which corresponds to a steam saturation temperature of 167-176°C. Material was fed at an average rate of 11 ODMT/day to the ˜1000 Ldigestor through a plug screw feeder (PSF) system with a compressionratio of approximately 8:1 or a rotary valve. The liquids to solidsratio feeding the digestor was 2.1:1. The residence time within thedigestor was 300-480 seconds.

The liquid pressate from the PSF was measured at a rate of approximately2 gallons per minute (gpm) (7.6 liters/minute) and contained free nitricacid (pH 1.3), as well as turpentine/tall oil type components (bysmell). In some cases, all of the liquid pressate was added back to thedigestor. In other cases, a portion of the liquid pressate was addedback to the digestor with the balance of the 2 gallons per minutesupplied by city water. In other cases, the PSF pressate was discardedand 2 gallons per minute of water were added to the digestor.

Pressure was maintained in the digestor with a 6 inch ball type blowvalve. The hydrolysate and residual solids were expanded to atmosphericpressure through a cyclone to separate the vapor from the liquid andsolids. Some volatiles were removed in the vent stream. Residual solidswere approximately 32% by weight.

A 560 screw press was used to attempt to separate solids from liquids.Very little dewatering was achieved. Average feed solids was measured atabout 36% and the residual solids exiting from the screw press wasmeasured to be 36-37%, due to the small average fiber dimension.

Surprisingly, the residual material had very little fiber quality orstructure. Microscopic imaging of the residual material showed littledistinguishable cellulosic fiber. The fiber had the followingcharacteristics:

Length weighted average length (mm) 0.276 Arithmetic average length (mm)0.151 Weight weighted average length (mm) 0.544 Average width (μm) 36.14Surface area (m²/kg) 1441Fiber Classifications

% on 14 mesh 0.5 % on 28 mesh 1.7 % on 48 mesh 3.7 % on 100 mesh 8.2 %on 200 mesh 9.6 % through 200 mesh 76.3 *% denotes weight fractionretained on the indicated mesh.

The hydrolysate liquor contained significant concentrations of primarilyhemicellulose sugars (˜75 g/L) in the ratios typical of softwood diluteacid hydrolysis: mannose, xylose, glucose, arabinose, and galactose.

In a follow up experiment, material that had been passed through thedisintegrator under conditions of either no acid added or 1.42% (w/w)nitric acid was reacted in a 7.6 liter Parr bomb type reactor. Noadditional water was added, in order to duplicate as closely as possiblethe conditions in the digestor (5 minutes, 166° C.). In this run, 750 gof the moist feed (36.8% solids by weight) were added. 450 g of waterwere also added to the reactor. Live steam was added until the reactorreached the setpoint temperature at which point the blow valve wasreleased (5 minutes) and the material was blown into a blow tank wherethe pressure was permitted to equilibrate with the environment.

The results are shown in FIG. 13. The residual solids from the no acidcondition are shown in the photograph on the left, and the residualsolids produced with 1.42% nitric acid are shown in the photograph onthe right. Visible cellulosic fiber was observed in the no acid samplebut not in the nitric acid sample.

Example 8 Hemicellulose Extraction from Wood Chips

Grey stage Lodgepole pine chips, moisture content approximately 31.6%,were passed through a thermomechanical disintegrator, as described inExample 1 except that the wood chips were not screened for debris andthe flow restriction at the exit of the disintegrator was 0.5 inch.

0.44% (w/w) nitric acid was added to the solid material at the exit ofthe RT Impressifiner and resulted in a 33.0% (w/w) solid discharge. Thematerial was fed to a digestor as described in Example 1, with storagefrom 1 to 12 hours prior to processing. The digestor conditions were asdescribed in Example 1, except the residence time was 360 seconds. NoPSF pressate was retained in the process, but water was added to therotary feeder (˜1.9 gpm) parallel to the PSF, the mechanical refiner(post digestor, between the digestor and the blow valve) (˜3 gpm), andthe discharge cyclone, which is located post blow valve.

The resulting visible fiber quality was greater than in the productdescribed in Example 1, and was effectively dewatered in the screwpress. Residual solids were 57.7% by weight.

The fiber had the following characteristics:

Length weighted average length (mm) 0.379 Arithmetic average length (mm)0.202 Weight weighted average length (mm) 0.862 Average width (μm) 49.72Surface area (m²/kg) 1105Fiber Classifications

% on 14 mesh 11.6 % on 28 mesh 18.0 % on 48 mesh 19.7 % on 100 mesh 20.2% on 200 mesh 7.4 % through 200 mesh 23.1 *% denotes weight fractionretained on the indicated mesh.

The hydrolysate liquor contained significant concentrations ofhemicellulose sugars (˜43.5 g/L) in the ratios typical of softwooddilute acid hydrolysis: mannose, xylose, glucose, arabinose, andgalactose.

Example 9 Continuous Fermentation of Clostridium Immobilized in a 1Liter Packed Bed Bioreactor for 422 Hours with Conditioned Hydrolysate

A butanol-producing Clostridium strain was grown anaerobically in apacked bed bioreactor with 1 L nominal volume and 670 mL working volume.The L/D ratio of the bioreactor was 3.

The Clostridium was immobilized on bonechar. The bonechar particles hada size of 3000 to 5000 microns, with a bulk density of about 0.72/ml.About 1.5 pounds of bonechar was loaded into the reactor. Immobilizationwas achieved by first filling the reactor with about 670 mL of CP3 mediawith 6% w/v softwood sugars synthetic mix (20.04% w/w D-glucose, 31.32%w/w D-xylose, 12.88% w/w L-arabinose, 35.76% w/w D-mannose) and thenadding to the reactor 60 mL of Clostridium broth that had an OD at 600nm of about 0.8, and recirculating the contents of the reactor for 24hours.

The initial growth medium as well as the medium used during thecontinuous part of the fermentation, contained conditioned beetle killedlodgepole pine acid hydrolysate with about 45 g/L sugar, supplementedwith P2 medium components and trace elements, except that ammonium wasadded as ammonium sulfate instead of as ammonium acetate. Thehydrolysate was prepared as described in Example 7, and conditioned onDuolite A7 resin at acidic pH.

Continuous culture was started around 21 hours after inoculation bypumping the growth media at a constant rate into the bottom of thebioreactor and continuously removing broth from the top of thebioreactor in order to maintain a constant liquid level in thebioreactor. Continuous fermentation continued for 422 hours.

The feed rate for the run was 8 g/min and N2 was added at a rate of 0.1L/min for the duration of the fermentation. During the fermentationperiod between 164 and 422 hours the average pH was about 5.1. Theaverage butanol titer, productivity, and yield were 7.6 g butanol/L, 5.5g butanol/L/hr, and 0.26 g butanol/g carbohydrate, respectively.

Example 10 Production of Multiple Bioproducts in a ContinuousImmobilized Microbial Fermentation

Clostridium was grown anaerobically in a packed bed bioreactor with111.3 L nominal volume and 65.7 L working volume. The L/D ratio of thebioreactor was 5.7.

The Clostridium was immobilized on bonechar initially screened with a5×8 mesh, with a bulk density of about 45 lb/ft3. About 100 pounds ofbonechar was loaded into the reactor Immobilization was achieved byfirst filling the reactor with about 100 L of fermentation media with 4%by weight softwood hydrolysate, prepared as described in Example 8 andconditioned on Duolite A7 resin at acidic pH, draining approximately 15L of feed media and then adding to the reactor about 15 L of Clostridiumbroth that had A600 absorbance of about 1. The fermentation broth wascirculated for approximately 24 h prior to setting the reactor intocontinuous operation.

Continuous culture was achieved after the bioreactor had been inoculatedby pumping the growth media at a constant rate into the bottom of thebioreactor and continuously removing broth from the top of thebioreactor in order to maintain a constant liquid level in thebioreactor.

The feed rate for the run was about 540 g/min. The average pH was about5.5 and the average pressure was about 3.4 psi. N2 was added at a rateof 1.0 L/min for the duration of the fermentation. After 106 hourselapsed fermentation time, yield of butanol, acetone, ethanol, aceticacid, and butyric acid were 0.220, 0.050, 0.020, 0.015, and 0.111 g/gsugars converted, respectively. Sugar conversion in the reactor variedthroughout the run and was approximately 50-80%.

Example 11 Purification of Biobutanol from Fermentation Broth

Fermentation broth from a continuous culture of immobilized Clostridium,grown in a packed bed bioreactor with 111.3 L nominal volume, 73.4 Lworking or packed bed volume, and L/D ratio (packed section) 5.7, wascollected from the bioreactor and pumped into a 500 gallon harvest tank.The residence time in the harvest tank was about 60 h, depending on thebioreactor harvest rate. When sufficient material had been collected, amicrofiltration step (2″×3′ microfiltration membrane unit, 0.1 umcutoff) was performed to remove cell mass and other debris.

The material was then transferred to a 75 gallon steam heated batchdistillation vessel with an insulated, packed overhead 4″ column toprovide some reflux. The vessel was indirectly heated with steam and theoverheads were condensed and collected by a receiver. Vessel pressurewas maintained at ambient pressure. Upon discharge from the receiver,the material was decanted and the butanol rich organic phase (60-80%BuOH by weight) was further distilled in a smaller, electrically heated5-stage Snyder distillation apparatus. The aqueous butanol phase (7-9%BuOH by weight) was discarded rather than subsequently separated.Recovery yield was 12%.

Preliminary analytical results for biobutanol derived from simple sugars(5% hardwood synthetic mix (9.0 g/l glucose, 32.8 g/l xylose, 5.8 g/larabinose, 3.3 g/l mannose)+1 g/L yeast extract, 2.2 g/L ammoniumacetate, 1 g/L K₂HPO₄, 0.1 g/L KH₂PO₄)), as described in this example,are presented in Table 2.

TABLE 2 Composition of Purified Biobutanol Butanol Water Acetic AcidButyric Acid (v/v %) (w/w %) (v/v %) (v/v %) 98.2 0.67 0.03 0.03

Although the foregoing invention has been described in some detail byway of illustration and examples for purposes of clarity ofunderstanding, it will be apparent to those skilled in the art thatcertain changes and modifications may be practiced without departingfrom the spirit and scope of the invention. Therefore, the descriptionand claims should not be construed as limiting the scope of theinvention.

All publications, patents, and patent applications cited herein arehereby incorporated by reference in their entireties for all purposesand to the same extent as if each individual publication, patent, orpatent application were specifically and individually indicated to be soincorporated by reference.

While preferred embodiments of the present invention have been shown anddescribed herein, it will be obvious to those skilled in the art thatsuch embodiments are provided by way of example only. Numerousvariations, changes, and substitutions will now occur to those skilledin the art without departing from the invention. It should be understoodthat various alternatives to the embodiments of the invention describedherein may be employed in practicing the invention. It is intended thatthe following claims define the scope of the invention and that methodsand structures within the scope of these claims and their equivalents becovered thereby.

What is claimed is:
 1. A system for production of a bioproduct,comprising a feedstock hydrolysis unit and a bioreactor, wherein acarbon-containing feedstock is continuously hydrolyzed in saidhydrolysis unit and the hydrolyzed feedstock is continuously fed to thebioreactor, wherein said bioreactor comprises a fermenting microorganismimmobilized on a support, wherein said hydrolysis of the feedstockproduces carbohydrate molecules that serve as a carbon source for saidfermentation, wherein the microorganism continuously converts thehydrolyzed feedstock into a bioproduct, and wherein said feedstockmaterial is deconstructed prior to hydrolysis.
 2. A system according toclaim 1, wherein said feedstock hydrolysis unit and said bioreactor arein fluid communication, wherein said hydrolysis unit is upstream fromsaid bioreactor, and wherein the feedstock is continuously hydrolyzedand continuously fed to the bioreactor for the duration of thefermentation.
 3. A system according to claim 2, comprising multiplebioreactors arranged in parallel, wherein said multiple bioreactors arein fluid communication with said hydrolysis unit, wherein the hydrolyzedfeedstock is fed continuously into said bioreactors, wherein thefermentation of the microorganism occurs continuously in saidbioreactors, and wherein the multiple bioreactors comprise the same ordifferent microorganism(s).
 4. A system according to claim 2, comprisingmultiple bioreactors arranged in series, wherein the first bioreactor inthe series is in fluid communication with the hydrolysis unit and with adownstream bioreactor, wherein each subsequent bioreactor in the seriesdownstream from the first bioreactor is in fluid communication with theprevious upstream bioreactor in the series, wherein the hydrolyzedfeedstock is fed continuously into the first bioreactor in the series,and wherein effluent from each bioreactor is fed to the next bioreactordownstream in the series.
 5. A system according to claim 1, wherein saidfeedstock is a cellulosic material.
 6. A system according to claim 5,wherein said feedstock is a lignocellulosic material.
 7. A systemaccording to claim 6, wherein said lignocellulosic material ispretreated to remove extractives.
 8. A system according to claim 7,wherein said pretreatment to remove extractives comprises compression,water extraction, solvent extraction, alkaline extraction, enzymatictreatment, fungal treatment, oxygen treatment, or air drying, whereinsaid pretreatment occurs prior to or in conjunction with deconstruction.9. A system according to claim 6, wherein said lignocellulosic materialcomprises wood chips, sawdust, saw mill residue, or a combinationthereof.
 10. A system according to claim 6, wherein said lignocellulosicmaterial is wood selected from softwood, hardwood, or a combinationthereof.
 11. A system according to claim 6, wherein said lignocelluosicmaterial is from a feedstock source that has been subjected to a diseaseor infestation.
 12. A system according to claim 6, wherein saidlignocellulosic material is deconstructed prior to harvest, wherein saiddeconstruction occurs due to one or more natural or intentional causescomprising drought, infestation, fire, or herbicide.
 13. A systemaccording to claim 6, wherein said lignocellulosic material comprisesbagasse or straw.
 14. A system according to claim 5, wherein saidfeedstock comprises cellulose and hemicellulose.
 15. A system accordingto claim 1, wherein said deconstruction process comprises one or moreprocess selected from presteaming, mechanical grinding, mechanicalexplosion, or a combination thereof.
 16. A system according to claim 1,wherein said hydrolysis is performed by treatment with one or more acid.17. A system according to claim 16, wherein said acid comprises nitricacid, formic acid, acetic acid, phosphoric acid, hydrochloric acid, orsulfuric acid.
 18. A system according to claim 17, wherein saidhydrolysis is performed with nitric acid.
 19. A system according toclaim 18, wherein said hydrolysis unit comprises a first hydrolysismodule and a second hydrolysis module, wherein nitric acid hydrolysiscomprises a first stage in the first hydrolysis module and a secondstage in the second hydrolysis module, and wherein the temperature ofthe nitric acid in the first hydrolysis module is higher than thetemperature of the nitric acid in the second hydrolysis module.
 20. Asystem according to claim 19, wherein the hydrolysis product streamsfrom the first and second hydrolysis modules are combined prior tointroduction into the bioreactor.
 21. A system according to claim 19,wherein the hydrolysis product streams from the first and secondhydrolysis modules are introduced as separate hydrolyzed feedstockstreams into separate bioreactors, wherein the first stage hydrolysateis introduced into a first bioreactor and the second stage hydrolysateis introduced into a second bioreactor, wherein the first and secondbioreactors comprise the same or different microorganism(s).
 22. Asystem according to claim 21, wherein the first bioreactor comprises afirst microorganism and the second bioreactor comprises a secondmicroorganism, wherein the first and second microorganisms aredifferent, and wherein the first microorganism is optimized for growthand/or desired product production on the first stage hydrolysate and thesecond microorganism is optimized for growth and/or desired productproduction on the second stage hydrolysate.
 23. A system according toclaim 19, wherein flash steam is generated during the hydrolysisprocess, and wherein said flash steam is used to provide energy for oneor more processes selected from deconstruction of said feedstock priorto hydrolysis, further hydrolysis of feedstock, and purification of thebioproduct.
 24. A system according to claim 19, wherein flash steam isgenerated in said second stage hydrolysis, and wherein said flash steamis provided to the feedstock for deconstruction of said feedstock priorto hydrolysis and/or to said first hydrolysis module to provide energyfor said first stage hydrolysis.
 25. A system according to claim 19,wherein flash steam is generated in said second stage hydrolysis,wherein said flash steam is recompressed, and wherein said recompressedsteam is provided to said first hydrolysis module to provide energy forsaid first stage hydrolysis and/or a downstream distillation process forproduct purification.
 26. A system according to claim 19, wherein flashsteam is generated in said second stage hydrolysis, wherein said flashsteam is provided to a third hydrolysis module to provide energy for athird stage hydrolysis, wherein the temperature in the third hydrolysismodule is lower than the temperature in the second hydrolysis module,and wherein said lower temperature permits hydrolysis of remainingoligomeric sugar molecules with less degradation than hydrolysisperformed at a higher temperature.
 27. A system according to claim 19,wherein hydrolysis of the feedstock produces a lignin-containingresidue, and wherein the lignin-containing residue is used as an energysource for said process and/or for electricity generation.
 28. A systemaccording to claim 19, further comprising a conditioning unit, whereinsaid conditioning unit is in fluid communication with both thehydrolysis unit and the bioreactor, wherein said conditioning unit isdownstream from the hydrolysis unit and upstream from the bioreactor,wherein hydrolyzed feedstock is conditioned in the conditioning unit toremove inhibitors of microbial growth and/or bioproduct production priorto introduction of the hydrolyzed feedstock into the bioreactor.
 29. Asystem according to claim 28, wherein the hydrolysis and conditioningprocesses occur continuously for the duration of the fermentation.
 30. Asystem according to claim 28, wherein removal of inhibitors comprisesone or more process(as) selected from overliming, adsorption, and ionexchange.
 31. A system according to claim 30, wherein said conditioningunit comprises an ion exchange resin, wherein removal of inhibitors isperformed by contact of hydrolyzed feedstock with the ion exchange resinunder conditions wherein the inhibitors are retained on the resin.
 32. Asystem according to claim 30, wherein removal of inhibitors is performedby precipitation with an aluminum or iron salt.
 33. A system accordingto claim 1, wherein the fermentation is conducted under anaerobicconditions.
 34. A system according to claim 33, wherein themicroorganism is a Clostridium strain.
 35. A system according to claim34, wherein the Clostridium strain is derived from a species selectedfrom Clostridium saccharobutylicum, Clostridiumsaccharoperbutylacetonicum, Clostridium acetobutylicum, Clostridiumbeijerinckii, Clostridium puniceum, Clostridium aurantibutyricum,Clostridium tetanomorphum, Clostridium thermosaccharolyticum,Clostridium butyricum, Clostridium cellulolyticum, Clostridiumphytofermentans, Clostridium thermohydrosulfuricum, Clostridiumthermobutyricum, Clostridium thermocellum, and Clostridium pasteurianum.36. A system according to claim 34, wherein the Clostridium strain is anenvironmental isolate or is derived from an environmental isolate.
 37. Asystem according to claim 1, wherein the support on which themicroorganism is immobilized on a support material selected from bonechar, polypropylene, steel, diatomaceous earth, zeolite, ceramic,engineered thermal plastic, clay brick, concrete, lava rock, wood chips,polyester fiber, glass beads, Teflon, polyetheretherketone, andpolyethylene.
 38. A system according to claim 1, wherein the immobilizedmicroorganism comprises a biofilm.
 39. A system according to claim 1,wherein the bioreactor comprises a packed bed, an expanded bed, or afluidized bed.
 40. A system according to claim 1, wherein the bioreactoroperates under pressure to compress gas in the bioreactor.
 41. A systemaccording to claim 1, wherein said hydrolysis of the feedstock comprisesenzymatic hydrolysis.
 42. A system according to claim 1, wherein saidhydrolysis of the feedstock comprises autohydrolysis with acetic acidreleased by the feedstock.
 43. A system according to claim 1, whereinthe bioproduct comprises a biofuel selected from butanol, acetone,ethanol, or a combination thereof.
 44. A system according to claim 43,wherein the biofuel comprises butanol.
 45. A system according to claim44, further comprising a recovery unit for recovery of butanol from thefermentation medium, wherein said recovery comprises distillation toseparate the butanol from other components of the fermentation medium.46. A system according to claim 45, wherein butyric acid is recovered insaid distillation, and wherein said butyric acid is added to thefermentation medium in said bioreactor, wherein said microorganismconverts said butyric acid to butanol.
 47. A system according to claim45, wherein flash steam is generated during hydrolysis of the feedstockand said flash steam provides energy for said distillation.
 48. A systemaccording to claim 1, further comprising a recovery unit for recovery ofthe bioproduct from the fermentation medium.
 49. A system according toclaim 48, wherein the recovery unit is in fluid communication with anddownstream from the bioreactor, wherein the recovery process operatescontinuously for the duration of the fermentation.
 50. A systemaccording to claim 48, wherein the recovery unit comprises aconcentration module for concentration of the bioproduct.
 51. A systemaccording to claim 50, wherein the recovery unit comprises adistillation module to separate the bioproduct from other components ofthe fermentation medium, wherein the distillation module is in fluidcommunication with and downstream from the concentration module.
 52. Asystem according to claim 48, wherein bioproduct-containing effluent iscontinuously withdrawn from the bioreactor, and wherein the byproduct isrecovered from the effluent in the recovery unit.